Multiplex sample analysis:Article Title: Subversion of kynurenine-induced AHR activation in CD8 T cells by kynureninase-expressing antigen-presenting cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TMT 10-plex Thermo Scientific Cat# 90110 TMT 11-plex reagent (131C) Thermo Scientific Cat# A37724 Hydroxylamine Sigma-Aldrich Cat# 159417 Critical commercial assays Griess Reagent Kit Promega Cat# G2930 Lung Dissociation Kit Miltenyi Biotec Cat# 130-095-927 Dead Cell Removal Kit Miltenyi Biotec Cat# 130-090-101 PureLink RNA Mini Kit Invitrogen Cat# 12183025 SYBR Green Master Mix Miltenyi Biotec Cat# 130-052-301 gentleMACS Octo Dissociator Miltenyi Biotec Cat# 130-095-937 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 KAPA HotStart Mouse Genotyping Kit Sigma-Aldrich Cat# KK7351 Mouse Th1/Th2/Th17 Array Q1 RayBiotech Cat# QAM-TH17-1-1 Mouse IFN-gamma R1 DuoSet ELISA R&D systems Cat# DY1026 Deposited data Metabolomics LC MS raw data Mass Spectrometry Interactive Virtual Environment (MassIVE) (https://massive.ucsd.edu) MassIVE: MSV000100659 Mass spectrometry proteomics data https://www.proteomexchange.org/ ProteomeXchange: PXD074605 Experimental models: Cell lines TC1 Kromer lab N/A TC1IDO1 This paper N/A Experimental models: Organisms/strains Mouse: C57BL6/J (WT) Charles River Laboratory N/A Mouse: C57BL/6NJ-KYNUem1(IMPC)J/J (KYNUem1) The Jackson Laboratory N/A Mouse: B6.129-Ahrtm1Bra/J The Jackson Laboratory N/A Mouse: C57BL/6-Tg(TcraTcrb)1100Mjb/J The Jackson Laboratory N/A Oligonucleotides See Document S1 for mouse gene-specific primers used for qRT-PCR N/A Recombinant DNA pLJM1-EGFP Addgene Plasmid #19319 pLJM1-Ido1 This paper N/A Software and algorithms Image Lab (Version 6.1) Bio-Rad https://www.bio-rad.com/ Graphpad Prism 9 Graphpad https://www.graphpad.com/ Seahorse Wave Controller Software (version 2.4.2) Agilent https://www.agilent.com/ Compound Discoverer Thermo Fisher Scientific https://mycompounddiscoverer.com/ R Studio R https://www.rstudio.com/ Adobe Illustrator Adobe https://www.adobe.com Bio-Rad CFX Manager Bio-Rad https://www.bio-rad.com/ Maven Maven N/A Skyline MacCoss Lab Software https://skyline.ms/project/home/begin.view FCS Express 7 Flow Research Edition DeNovo Software https://denovosoftware.com/ BioRender BioRender https://biorender.com/ Sequest Thermo Fisher https://proteomicsresource.washington.edu/ protocols06/sequest.php Other QExactive Mass Spectrometer Thermo Fisher Scientific N/A (Continued on next page) 22 Cell Reports 45, 117149, April 28, 2026 .. C57BL6/J (WT) mice were obtained from Charles River Laboratories.
SYBR Green Assay:Article Title: Subversion of kynurenine-induced AHR activation in CD8 T cells by kynureninase-expressing antigen-presenting cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TMT 10-plex Thermo Scientific Cat# 90110 TMT 11-plex reagent (131C) Thermo Scientific Cat# A37724 Hydroxylamine Sigma-Aldrich Cat# 159417 Critical commercial assays Griess Reagent Kit Promega Cat# G2930 Lung Dissociation Kit Miltenyi Biotec Cat# 130-095-927 Dead Cell Removal Kit Miltenyi Biotec Cat# 130-090-101 PureLink RNA Mini Kit Invitrogen Cat# 12183025 SYBR Green Master Mix Miltenyi Biotec Cat# 130-052-301 gentleMACS Octo Dissociator Miltenyi Biotec Cat# 130-095-937 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 KAPA HotStart Mouse Genotyping Kit Sigma-Aldrich Cat# KK7351 Mouse Th1/Th2/Th17 Array Q1 RayBiotech Cat# QAM-TH17-1-1 Mouse IFN-gamma R1 DuoSet ELISA R&D systems Cat# DY1026 Deposited data Metabolomics LC MS raw data Mass Spectrometry Interactive Virtual Environment (MassIVE) (https://massive.ucsd.edu) MassIVE: MSV000100659 Mass spectrometry proteomics data https://www.proteomexchange.org/ ProteomeXchange: PXD074605 Experimental models: Cell lines TC1 Kromer lab N/A TC1IDO1 This paper N/A Experimental models: Organisms/strains Mouse: C57BL6/J (WT) Charles River Laboratory N/A Mouse: C57BL/6NJ-KYNUem1(IMPC)J/J (KYNUem1) The Jackson Laboratory N/A Mouse: B6.129-Ahrtm1Bra/J The Jackson Laboratory N/A Mouse: C57BL/6-Tg(TcraTcrb)1100Mjb/J The Jackson Laboratory N/A Oligonucleotides See Document S1 for mouse gene-specific primers used for qRT-PCR N/A Recombinant DNA pLJM1-EGFP Addgene Plasmid #19319 pLJM1-Ido1 This paper N/A Software and algorithms Image Lab (Version 6.1) Bio-Rad https://www.bio-rad.com/ Graphpad Prism 9 Graphpad https://www.graphpad.com/ Seahorse Wave Controller Software (version 2.4.2) Agilent https://www.agilent.com/ Compound Discoverer Thermo Fisher Scientific https://mycompounddiscoverer.com/ R Studio R https://www.rstudio.com/ Adobe Illustrator Adobe https://www.adobe.com Bio-Rad CFX Manager Bio-Rad https://www.bio-rad.com/ Maven Maven N/A Skyline MacCoss Lab Software https://skyline.ms/project/home/begin.view FCS Express 7 Flow Research Edition DeNovo Software https://denovosoftware.com/ BioRender BioRender https://biorender.com/ Sequest Thermo Fisher https://proteomicsresource.washington.edu/ protocols06/sequest.php Other QExactive Mass Spectrometer Thermo Fisher Scientific N/A (Continued on next page) 22 Cell Reports 45, 117149, April 28, 2026 .. C57BL6/J (WT) mice were obtained from Charles River Laboratories.
Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Article Title: Circuit and molecular mechanisms underlying incubation of methamphetamine craving in the prelimbic cortex.
Article Snippet: Article Circuit and molecular mechanisms underlying incubation of methamphetamine craving in the prelimbic cortex Highlights • SST and PV interneurons in the PL differentially regulate methamphetamine craving • LHGABA → PLSST and AMGlu → PLPV circuits drive stagespecific craving • KCNC2 upregulation in interneurons underlies distinct neuronal excitability changes • Specific knockdown of KCNC2 reduces craving during early and prolonged withdrawal Authors Sai Shi, Yi-Wen Sun, Jin-Jun Ding, ..., Fang Liu, Ti-Fei Yuan, Min Zhao Correspondence fang.liu@camh.ca (F.L.), ytf0707@126.com (T..-F.Y.), drminzhao@smhc.org.cn (M.Z.). In brief Shi et al. reveal that two distinct interneurons in the PL control the incubation of methamphetamine craving during different withdrawal stages.. They uncover a circuit-switch principle and propose a key molecular mediator, offering phase-specific therapeutic strategies to reduce relapse.
Bicinchoninic Acid Protein Assay:Article Title: Subversion of kynurenine-induced AHR activation in CD8 T cells by kynureninase-expressing antigen-presenting cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TMT 10-plex Thermo Scientific Cat# 90110 TMT 11-plex reagent (131C) Thermo Scientific Cat# A37724 Hydroxylamine Sigma-Aldrich Cat# 159417 Critical commercial assays Griess Reagent Kit Promega Cat# G2930 Lung Dissociation Kit Miltenyi Biotec Cat# 130-095-927 Dead Cell Removal Kit Miltenyi Biotec Cat# 130-090-101 PureLink RNA Mini Kit Invitrogen Cat# 12183025 SYBR Green Master Mix Miltenyi Biotec Cat# 130-052-301 gentleMACS Octo Dissociator Miltenyi Biotec Cat# 130-095-937 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 KAPA HotStart Mouse Genotyping Kit Sigma-Aldrich Cat# KK7351 Mouse Th1/Th2/Th17 Array Q1 RayBiotech Cat# QAM-TH17-1-1 Mouse IFN-gamma R1 DuoSet ELISA R&D systems Cat# DY1026 Deposited data Metabolomics LC MS raw data Mass Spectrometry Interactive Virtual Environment (MassIVE) (https://massive.ucsd.edu) MassIVE: MSV000100659 Mass spectrometry proteomics data https://www.proteomexchange.org/ ProteomeXchange: PXD074605 Experimental models: Cell lines TC1 Kromer lab N/A TC1IDO1 This paper N/A Experimental models: Organisms/strains Mouse: C57BL6/J (WT) Charles River Laboratory N/A Mouse: C57BL/6NJ-KYNUem1(IMPC)J/J (KYNUem1) The Jackson Laboratory N/A Mouse: B6.129-Ahrtm1Bra/J The Jackson Laboratory N/A Mouse: C57BL/6-Tg(TcraTcrb)1100Mjb/J The Jackson Laboratory N/A Oligonucleotides See Document S1 for mouse gene-specific primers used for qRT-PCR N/A Recombinant DNA pLJM1-EGFP Addgene Plasmid #19319 pLJM1-Ido1 This paper N/A Software and algorithms Image Lab (Version 6.1) Bio-Rad https://www.bio-rad.com/ Graphpad Prism 9 Graphpad https://www.graphpad.com/ Seahorse Wave Controller Software (version 2.4.2) Agilent https://www.agilent.com/ Compound Discoverer Thermo Fisher Scientific https://mycompounddiscoverer.com/ R Studio R https://www.rstudio.com/ Adobe Illustrator Adobe https://www.adobe.com Bio-Rad CFX Manager Bio-Rad https://www.bio-rad.com/ Maven Maven N/A Skyline MacCoss Lab Software https://skyline.ms/project/home/begin.view FCS Express 7 Flow Research Edition DeNovo Software https://denovosoftware.com/ BioRender BioRender https://biorender.com/ Sequest Thermo Fisher https://proteomicsresource.washington.edu/ protocols06/sequest.php Other QExactive Mass Spectrometer Thermo Fisher Scientific N/A (Continued on next page) 22 Cell Reports 45, 117149, April 28, 2026 .. C57BL6/J (WT) mice were obtained from Charles River Laboratories.
Article Title: The insertion of an ATTTC repeat in an Alu element hyperactivates a neurodevelopmental enhancer in spinocerebellar ataxia type 37.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nano-Glo® Dual-Luciferase® Reporter Assay System Promega Cat #N1610 NZYMiniprep Kit NZYtech Cat #MB01002 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat #23227 PSC 4-Marker Immunocytochemistry Kit Thermo Fisher Scientific Cat #A24881 PureLinkTM RNA Micro Scale Kit Thermo Fisher Scientific Cat #12183016 QIAquick Gel Extraction Kit Zymoclean Gel DNA Recovery Kit QIAGEN Cat #28704 Quick-DNA Miniprep Kit ZYMO Research Cat #D4068S RNA Clean & Concentrator kit ZYMO Research Cat #R1017 RNeasy Mini Kit Qiagen Cat #74104 SuperScript III First-Strand Synthesis SuperMix for qRT-PCR Thermo Fisher Scientific Cat #11752050 Zymoclean Gel DNA Recovery Kit ZYMO Research Cat #D4008 Deposited data H3K27ac ChiP-seq in Acute myeloid leukemia ChiP-Atlas SRX13109961 H3K27ac ChiP-seq in CD4+ ChiP-Atlas SRX5944575 H3K27ac ChiP-seq in cerebellum ChiP-Atlas SRX5806022 GSM3755478 H3K27ac ChiP-seq in cerebellum ChiP-Atlas SRX263277 GSM1119154 H3K27ac ChiP-seq in GI-ME-N ChiP-Atlas SRX8887748 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX7805843 GSM4340237 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX7805844 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX8806625 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX8806626 H3K27ac ChiP-seq in Jurkat ChiP-Atlas SRX2022917 H3K27ac ChiP-seq in Lymphoma B-cell ChiP-Atlas SRX4277998 H3K27ac ChiP-seq in Melanoma ChiP-Atlas SRX685325 GSM1484301 H3K27ac ChiP-seq in MUG-Chor1 ChiP-Atlas SRX3623423 H3K27ac ChiP-seq in PSC-derived hepatocyte-like ChiP-Atlas SRX12495361 H3K27ac ChiP-seq in PSC-derived hepatocyte-like ChiP-Atlas SRX12495362 H3K27ac ChiP-seq in T-All ChiP-Atlas SRX3216827 H3K4me1 ChiP-seq in ESC ChiP-Atlas SRX2881133 GSM2648927 H3K4me1 ChiP-seq in HepG2 ChiP-Atlas SRX3733792 H3K4me1 ChiP-seq in hESC-derived cardiac cell ChiP-Atlas SRX13466352 H3K4me1 ChiP-seq in IMR-90 ChiP-Atlas SRX119737 GSM873694 H3K4me1 ChiP-seq in iPSC ChiP-Atlas SRX8806628 H3K4me3 ChiP-seq in CD34+ ChiP-Atlas ERX690596 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299240 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299242 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299244 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299245 H3K4me3 ChiP-seq in iSLK ChiP-Atlas SRX503343 H3K4me3 ChiP-seq in neural progenitors ChiP-Atlas SRX8997967 Hi-C data of human cerebellum 28 ENCODE DCC-2017 (Continued on next page) 22 Cell Reports 45, 117146, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: cell lines Control iPS cell line GM23280 Coriell Institute Cat #GM23280 Control iPS cell line NAS6 gift from Dr T. Kunath, University of Edinburgh; Ludtmann et al.60 N/A Control iPS cell line ND41866 Coriell Institute Cat #ND41866 Fibroblast cell line AF2 Seixas et al.8 N/A Fibroblast cell line AF3 Seixas et al.8 N/A Fibroblast cell line AF4 Seixas et al.8 N/A Human embryonic kidney 293T (HEK293T) cell line ATCC Cat #CRL-3216 Human neural stem cells (hNCS) Sun et al.61 N/A SCA37 iPS cell line AF2Cl21 This study N/A SCA37 iPS cell line AF2Cl4 This study N/A SCA37 iPS cell line AF3Cl7 This study N/A SCA37 iPS cell line AF4Cl32 This study N/A Experimental models: organisms/strains Transgenic zebrafish line gSA2AzGFF152B; UAS:GFP Kindly gift by Drs. Kawakami and Hibi, Japan; Takeuchi et al.47; Asakawa et al.62 N/A Transgenic zebrafish line Tg(Frag1:EGFP) This study N/A Transgenic zebrafish line Tg(Frag3:EGFP) This study N/A Transgenic zebrafish line Tg(FragT:EGFP) This study N/A Zebrafish WTAB This study N/A Oligonucleotides Primers for 4C-seq are provided in Table S2 This study N/A Primers for cloning FragT and subfragments in pMCS or Topo8 are provided in Table S2 This study N/A Primers for cloning TK promoter in pGL4.23-GW are provided in Table S2 This study N/A Primers for genotyping of HEK293T cell clones are provided in Table S2 This study N/A Primers for qPCR are provided in Table S2 This study N/A SgRNAs used for FragT deletion are provided in Table S3 This study N/A Recombinant DNA
Article Title: SenCat: Cataloging human cell senescence through multi-omic profiling of multiple senescent primary cell types.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins DMEM Gibco Cat# 11965092 FBS Gibco Cat# A5256801 Penicillin-Streptomycin Gibco Cat# 15140122 Nonessential Amino Acids (100X) Gibco Cat# 11140050 Antibiotic-antimycotic (100X) Gibco Cat# 15240062 Maxima Reverse Transcriptase Thermo Scientific Cat# EP0743 KAPA SYBR Fast ABI Master Mix (2X) Roche Cat# 07959435001 RiboLock RNase Inhibitor Invitrogen Cat# EO0381 Random Primers Invitrogen Cat# 48190011 dNTP Mix (10 mM each) Thermo Scientific Cat# R0192 Sodium pyruvate Gibco 11360070 RPMI 1640 Gibco 11875093 Ham’s F-10 medium Gibco 11550043 Doxorubicin Selleckchem S1208 Etoposide Selleckchem S1225 Triethylammonium bicarbonate Thermo Fisher Scientific Cat# 90114 Dithiothreitol Sigma-Aldrich Cat# D9779 Iodoacetamide Sigma-Aldrich Cat# I1149 Trypsin Promega Cat# V5113 Formic acid Sigma-Aldrich Cat# 27001 Nonidet P40 Substitute Sigma-Aldrich Cat# 74385 Critical commercial assays RLT Buffer QIAGEN 79216 RNeasy Plus Mini Kit QIAGEN 74136 TruSeq Stranded Total RNA Library Prep Kit Illumina Cat# 20020598 AMPure XP beads Beckman Coulter Cat# A63881 SPRIselect beads Beckman Coulter Cat# B23318 BrdU Cell Proliferation Assay Kit Cell Signaling Technology Cat# 6813 Senescence β-Galactosidase Staining Kit Cell Signaling Technology Cat# 9860 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 Oasis HLB Solid Phase Extraction Cartridges Waters Cat# 186000383 Minute Single Nucleus Isolation Kit for Tissues/Cells Invent Biotechnologies Cat# SN-047 Chromium GEM-X Single Cell 3’ Kit v4 10x Genomics PN-1000691 Chromium Single Cell 3’ Library Construction Kit C 10x Genomics PN-1000694 Deposited data Previously published and/or public datasets used GEO ProteomeXchange GSE247719; PXD058684 Bulk RNA-seq data generated in this study GEO GSE285826 snRNA-seq data from doxorubicintreated mice GEO GSE302792 (Continued on next page) ll OPEN ACCESSResource Molecular Cell 86, 1–12.e1–e8, July 2, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bulk proteomic raw data MassIVE MSV000096215 Original microscopy images Mendeley Data DOI: 10.17632/5wt4tzhs7z.1 snRNA-seq refinement, senescence calling, and bulk proteomic analysis code Zenodo 10.5281/zenodo.19203645; 10.5281/ zenodo.19204600 ML analysis code Zenodo / GitHub DOI: 10.5281/zenodo.19333691; DOI: 10.
Article Title: A human iPSC-derived sensory neuron platform for high-throughput discovery of neuroprotectants against chemotherapy-induced peripheral neuropathy.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER LIVE/DEAD far-red dye (LDR) Thermo Fisher Scientific Cat# L10120 Critical commercial assays Caspase-Glo® 3/7 Assay System Promega Cat# G8090 Pierce High-Select FeNTA Phosphopeptide Enrichment Kit Thermo Scientific Cat# A32992 MACS Embryoid Body Dissociation Kit Miltenyi Biotech Cat# 130-096-348 BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23235 Deposited data Bulk RNA Sequencing Data This paper GEO: GSE298389 Proteomic and Phosphoproteomic Data This paper ProteomeXchange Consortium via PRIDE (ID: PXD074954). .. Experimental models: Cell lines Human iPSC line LiPSC.GR-1.1 (male donor) NIH Common Fund (Regenerative Medicine Program) N/A Primary human DRG neurons AnaBios Corporation N/A iCell Sensory Neurons, Female FUJIFILM Cat# 21527 iCell Sensory Neurons, Male FUJIFILM Cat# 01279 MCF7 breast cancer cells ATCC HTB-22 BT20 breast cancer cells ATCC HTB-19 BT549 breast cancer cells ATCC HTB-122 Hs578 T breast cancer cells ATCC HTB-126 ReN VM neural progenitor cells EMD Millipore SCC008 Experimental models: Organisms/strains Mouse: A/J (Strain 646) Jackson Laboratory 000646 Oligonucleotides siRNA against MAP4K6 (MINK1) Thermo Fisher Scientific Cat# s27006 siRNA against MAP4K7 (TNIK) Thermo Fisher Scientific Cat# s22905 siRNA against MAP4K4 (HGK) Thermo Fisher Scientific Cat# s18096 Software and algorithms Custom Analysis Code This paper https://github.com/labsyspharm/ peripheral-neuropathy MetaXpress Custom Module Editor Molecular Devices RRID: SCR_016654 IncuCyte Sartorius RRID: SCR_025411 GraphPad Prism GraphPad RRID: SCR_002798 Seaborn (Python) https://doi.org/10.21105/joss.03021 RRID: SCR_018132 fgsea v1.32.4 https://doi.org/10.1101/060012 RRID: SCR_020938 DESeq2 v1.46.0 https://doi.org/10.1186/s13059-014-0550-8 RRID: SCR_015687 limma v3.62.2 https://doi.org/10.1093/nar/gkv007 RRID: SCR_010943 Salmon v1.10.3 https://doi.org/10.1038/nmeth.4197 RRID: SCR_017036 tximport v1.34.0 https://doi.org/10.12688/f1000research.7563.1 RRID: SCR_016752 msigdbr v24.1.0 https://doi.org/10.1016/J.CELS.2015.12.004 RRID: SCR_022870 R v4.4.2 R project RRID: SCR_001905 Cell Reports Medicine 7, 102787, May 19, 2026 e2 Article ll OPEN ACCESS plates at 37◦C and 5% CO2.
Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Article Title: Circuit and molecular mechanisms underlying incubation of methamphetamine craving in the prelimbic cortex.
Article Snippet: Article Circuit and molecular mechanisms underlying incubation of methamphetamine craving in the prelimbic cortex Highlights • SST and PV interneurons in the PL differentially regulate methamphetamine craving • LHGABA → PLSST and AMGlu → PLPV circuits drive stagespecific craving • KCNC2 upregulation in interneurons underlies distinct neuronal excitability changes • Specific knockdown of KCNC2 reduces craving during early and prolonged withdrawal Authors Sai Shi, Yi-Wen Sun, Jin-Jun Ding, ..., Fang Liu, Ti-Fei Yuan, Min Zhao Correspondence fang.liu@camh.ca (F.L.), ytf0707@126.com (T..-F.Y.), drminzhao@smhc.org.cn (M.Z.). In brief Shi et al. reveal that two distinct interneurons in the PL control the incubation of methamphetamine craving during different withdrawal stages.. They uncover a circuit-switch principle and propose a key molecular mediator, offering phase-specific therapeutic strategies to reduce relapse.
Enzyme-linked Immunosorbent Assay:Article Title: Subversion of kynurenine-induced AHR activation in CD8 T cells by kynureninase-expressing antigen-presenting cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TMT 10-plex Thermo Scientific Cat# 90110 TMT 11-plex reagent (131C) Thermo Scientific Cat# A37724 Hydroxylamine Sigma-Aldrich Cat# 159417 Critical commercial assays Griess Reagent Kit Promega Cat# G2930 Lung Dissociation Kit Miltenyi Biotec Cat# 130-095-927 Dead Cell Removal Kit Miltenyi Biotec Cat# 130-090-101 PureLink RNA Mini Kit Invitrogen Cat# 12183025 SYBR Green Master Mix Miltenyi Biotec Cat# 130-052-301 gentleMACS Octo Dissociator Miltenyi Biotec Cat# 130-095-937 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 KAPA HotStart Mouse Genotyping Kit Sigma-Aldrich Cat# KK7351 Mouse Th1/Th2/Th17 Array Q1 RayBiotech Cat# QAM-TH17-1-1 Mouse IFN-gamma R1 DuoSet ELISA R&D systems Cat# DY1026 Deposited data Metabolomics LC MS raw data Mass Spectrometry Interactive Virtual Environment (MassIVE) (https://massive.ucsd.edu) MassIVE: MSV000100659 Mass spectrometry proteomics data https://www.proteomexchange.org/ ProteomeXchange: PXD074605 Experimental models: Cell lines TC1 Kromer lab N/A TC1IDO1 This paper N/A Experimental models: Organisms/strains Mouse: C57BL6/J (WT) Charles River Laboratory N/A Mouse: C57BL/6NJ-KYNUem1(IMPC)J/J (KYNUem1) The Jackson Laboratory N/A Mouse: B6.129-Ahrtm1Bra/J The Jackson Laboratory N/A Mouse: C57BL/6-Tg(TcraTcrb)1100Mjb/J The Jackson Laboratory N/A Oligonucleotides See Document S1 for mouse gene-specific primers used for qRT-PCR N/A Recombinant DNA pLJM1-EGFP Addgene Plasmid #19319 pLJM1-Ido1 This paper N/A Software and algorithms Image Lab (Version 6.1) Bio-Rad https://www.bio-rad.com/ Graphpad Prism 9 Graphpad https://www.graphpad.com/ Seahorse Wave Controller Software (version 2.4.2) Agilent https://www.agilent.com/ Compound Discoverer Thermo Fisher Scientific https://mycompounddiscoverer.com/ R Studio R https://www.rstudio.com/ Adobe Illustrator Adobe https://www.adobe.com Bio-Rad CFX Manager Bio-Rad https://www.bio-rad.com/ Maven Maven N/A Skyline MacCoss Lab Software https://skyline.ms/project/home/begin.view FCS Express 7 Flow Research Edition DeNovo Software https://denovosoftware.com/ BioRender BioRender https://biorender.com/ Sequest Thermo Fisher https://proteomicsresource.washington.edu/ protocols06/sequest.php Other QExactive Mass Spectrometer Thermo Fisher Scientific N/A (Continued on next page) 22 Cell Reports 45, 117149, April 28, 2026 .. C57BL6/J (WT) mice were obtained from Charles River Laboratories.
Liquid Chromatography with Mass Spectroscopy:Article Title: Subversion of kynurenine-induced AHR activation in CD8 T cells by kynureninase-expressing antigen-presenting cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TMT 10-plex Thermo Scientific Cat# 90110 TMT 11-plex reagent (131C) Thermo Scientific Cat# A37724 Hydroxylamine Sigma-Aldrich Cat# 159417 Critical commercial assays Griess Reagent Kit Promega Cat# G2930 Lung Dissociation Kit Miltenyi Biotec Cat# 130-095-927 Dead Cell Removal Kit Miltenyi Biotec Cat# 130-090-101 PureLink RNA Mini Kit Invitrogen Cat# 12183025 SYBR Green Master Mix Miltenyi Biotec Cat# 130-052-301 gentleMACS Octo Dissociator Miltenyi Biotec Cat# 130-095-937 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 KAPA HotStart Mouse Genotyping Kit Sigma-Aldrich Cat# KK7351 Mouse Th1/Th2/Th17 Array Q1 RayBiotech Cat# QAM-TH17-1-1 Mouse IFN-gamma R1 DuoSet ELISA R&D systems Cat# DY1026 Deposited data Metabolomics LC MS raw data Mass Spectrometry Interactive Virtual Environment (MassIVE) (https://massive.ucsd.edu) MassIVE: MSV000100659 Mass spectrometry proteomics data https://www.proteomexchange.org/ ProteomeXchange: PXD074605 Experimental models: Cell lines TC1 Kromer lab N/A TC1IDO1 This paper N/A Experimental models: Organisms/strains Mouse: C57BL6/J (WT) Charles River Laboratory N/A Mouse: C57BL/6NJ-KYNUem1(IMPC)J/J (KYNUem1) The Jackson Laboratory N/A Mouse: B6.129-Ahrtm1Bra/J The Jackson Laboratory N/A Mouse: C57BL/6-Tg(TcraTcrb)1100Mjb/J The Jackson Laboratory N/A Oligonucleotides See Document S1 for mouse gene-specific primers used for qRT-PCR N/A Recombinant DNA pLJM1-EGFP Addgene Plasmid #19319 pLJM1-Ido1 This paper N/A Software and algorithms Image Lab (Version 6.1) Bio-Rad https://www.bio-rad.com/ Graphpad Prism 9 Graphpad https://www.graphpad.com/ Seahorse Wave Controller Software (version 2.4.2) Agilent https://www.agilent.com/ Compound Discoverer Thermo Fisher Scientific https://mycompounddiscoverer.com/ R Studio R https://www.rstudio.com/ Adobe Illustrator Adobe https://www.adobe.com Bio-Rad CFX Manager Bio-Rad https://www.bio-rad.com/ Maven Maven N/A Skyline MacCoss Lab Software https://skyline.ms/project/home/begin.view FCS Express 7 Flow Research Edition DeNovo Software https://denovosoftware.com/ BioRender BioRender https://biorender.com/ Sequest Thermo Fisher https://proteomicsresource.washington.edu/ protocols06/sequest.php Other QExactive Mass Spectrometer Thermo Fisher Scientific N/A (Continued on next page) 22 Cell Reports 45, 117149, April 28, 2026 .. C57BL6/J (WT) mice were obtained from Charles River Laboratories.
Mass Spectrometry:Article Title: Subversion of kynurenine-induced AHR activation in CD8 T cells by kynureninase-expressing antigen-presenting cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TMT 10-plex Thermo Scientific Cat# 90110 TMT 11-plex reagent (131C) Thermo Scientific Cat# A37724 Hydroxylamine Sigma-Aldrich Cat# 159417 Critical commercial assays Griess Reagent Kit Promega Cat# G2930 Lung Dissociation Kit Miltenyi Biotec Cat# 130-095-927 Dead Cell Removal Kit Miltenyi Biotec Cat# 130-090-101 PureLink RNA Mini Kit Invitrogen Cat# 12183025 SYBR Green Master Mix Miltenyi Biotec Cat# 130-052-301 gentleMACS Octo Dissociator Miltenyi Biotec Cat# 130-095-937 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 KAPA HotStart Mouse Genotyping Kit Sigma-Aldrich Cat# KK7351 Mouse Th1/Th2/Th17 Array Q1 RayBiotech Cat# QAM-TH17-1-1 Mouse IFN-gamma R1 DuoSet ELISA R&D systems Cat# DY1026 Deposited data Metabolomics LC MS raw data Mass Spectrometry Interactive Virtual Environment (MassIVE) (https://massive.ucsd.edu) MassIVE: MSV000100659 Mass spectrometry proteomics data https://www.proteomexchange.org/ ProteomeXchange: PXD074605 Experimental models: Cell lines TC1 Kromer lab N/A TC1IDO1 This paper N/A Experimental models: Organisms/strains Mouse: C57BL6/J (WT) Charles River Laboratory N/A Mouse: C57BL/6NJ-KYNUem1(IMPC)J/J (KYNUem1) The Jackson Laboratory N/A Mouse: B6.129-Ahrtm1Bra/J The Jackson Laboratory N/A Mouse: C57BL/6-Tg(TcraTcrb)1100Mjb/J The Jackson Laboratory N/A Oligonucleotides See Document S1 for mouse gene-specific primers used for qRT-PCR N/A Recombinant DNA pLJM1-EGFP Addgene Plasmid #19319 pLJM1-Ido1 This paper N/A Software and algorithms Image Lab (Version 6.1) Bio-Rad https://www.bio-rad.com/ Graphpad Prism 9 Graphpad https://www.graphpad.com/ Seahorse Wave Controller Software (version 2.4.2) Agilent https://www.agilent.com/ Compound Discoverer Thermo Fisher Scientific https://mycompounddiscoverer.com/ R Studio R https://www.rstudio.com/ Adobe Illustrator Adobe https://www.adobe.com Bio-Rad CFX Manager Bio-Rad https://www.bio-rad.com/ Maven Maven N/A Skyline MacCoss Lab Software https://skyline.ms/project/home/begin.view FCS Express 7 Flow Research Edition DeNovo Software https://denovosoftware.com/ BioRender BioRender https://biorender.com/ Sequest Thermo Fisher https://proteomicsresource.washington.edu/ protocols06/sequest.php Other QExactive Mass Spectrometer Thermo Fisher Scientific N/A (Continued on next page) 22 Cell Reports 45, 117149, April 28, 2026 .. C57BL6/J (WT) mice were obtained from Charles River Laboratories.
Quantitative RT-PCR:Article Title: Subversion of kynurenine-induced AHR activation in CD8 T cells by kynureninase-expressing antigen-presenting cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TMT 10-plex Thermo Scientific Cat# 90110 TMT 11-plex reagent (131C) Thermo Scientific Cat# A37724 Hydroxylamine Sigma-Aldrich Cat# 159417 Critical commercial assays Griess Reagent Kit Promega Cat# G2930 Lung Dissociation Kit Miltenyi Biotec Cat# 130-095-927 Dead Cell Removal Kit Miltenyi Biotec Cat# 130-090-101 PureLink RNA Mini Kit Invitrogen Cat# 12183025 SYBR Green Master Mix Miltenyi Biotec Cat# 130-052-301 gentleMACS Octo Dissociator Miltenyi Biotec Cat# 130-095-937 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 KAPA HotStart Mouse Genotyping Kit Sigma-Aldrich Cat# KK7351 Mouse Th1/Th2/Th17 Array Q1 RayBiotech Cat# QAM-TH17-1-1 Mouse IFN-gamma R1 DuoSet ELISA R&D systems Cat# DY1026 Deposited data Metabolomics LC MS raw data Mass Spectrometry Interactive Virtual Environment (MassIVE) (https://massive.ucsd.edu) MassIVE: MSV000100659 Mass spectrometry proteomics data https://www.proteomexchange.org/ ProteomeXchange: PXD074605 Experimental models: Cell lines TC1 Kromer lab N/A TC1IDO1 This paper N/A Experimental models: Organisms/strains Mouse: C57BL6/J (WT) Charles River Laboratory N/A Mouse: C57BL/6NJ-KYNUem1(IMPC)J/J (KYNUem1) The Jackson Laboratory N/A Mouse: B6.129-Ahrtm1Bra/J The Jackson Laboratory N/A Mouse: C57BL/6-Tg(TcraTcrb)1100Mjb/J The Jackson Laboratory N/A Oligonucleotides See Document S1 for mouse gene-specific primers used for qRT-PCR N/A Recombinant DNA pLJM1-EGFP Addgene Plasmid #19319 pLJM1-Ido1 This paper N/A Software and algorithms Image Lab (Version 6.1) Bio-Rad https://www.bio-rad.com/ Graphpad Prism 9 Graphpad https://www.graphpad.com/ Seahorse Wave Controller Software (version 2.4.2) Agilent https://www.agilent.com/ Compound Discoverer Thermo Fisher Scientific https://mycompounddiscoverer.com/ R Studio R https://www.rstudio.com/ Adobe Illustrator Adobe https://www.adobe.com Bio-Rad CFX Manager Bio-Rad https://www.bio-rad.com/ Maven Maven N/A Skyline MacCoss Lab Software https://skyline.ms/project/home/begin.view FCS Express 7 Flow Research Edition DeNovo Software https://denovosoftware.com/ BioRender BioRender https://biorender.com/ Sequest Thermo Fisher https://proteomicsresource.washington.edu/ protocols06/sequest.php Other QExactive Mass Spectrometer Thermo Fisher Scientific N/A (Continued on next page) 22 Cell Reports 45, 117149, April 28, 2026 .. C57BL6/J (WT) mice were obtained from Charles River Laboratories.
Article Title: The insertion of an ATTTC repeat in an Alu element hyperactivates a neurodevelopmental enhancer in spinocerebellar ataxia type 37.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nano-Glo® Dual-Luciferase® Reporter Assay System Promega Cat #N1610 NZYMiniprep Kit NZYtech Cat #MB01002 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat #23227 PSC 4-Marker Immunocytochemistry Kit Thermo Fisher Scientific Cat #A24881 PureLinkTM RNA Micro Scale Kit Thermo Fisher Scientific Cat #12183016 QIAquick Gel Extraction Kit Zymoclean Gel DNA Recovery Kit QIAGEN Cat #28704 Quick-DNA Miniprep Kit ZYMO Research Cat #D4068S RNA Clean & Concentrator kit ZYMO Research Cat #R1017 RNeasy Mini Kit Qiagen Cat #74104 SuperScript III First-Strand Synthesis SuperMix for qRT-PCR Thermo Fisher Scientific Cat #11752050 Zymoclean Gel DNA Recovery Kit ZYMO Research Cat #D4008 Deposited data H3K27ac ChiP-seq in Acute myeloid leukemia ChiP-Atlas SRX13109961 H3K27ac ChiP-seq in CD4+ ChiP-Atlas SRX5944575 H3K27ac ChiP-seq in cerebellum ChiP-Atlas SRX5806022 GSM3755478 H3K27ac ChiP-seq in cerebellum ChiP-Atlas SRX263277 GSM1119154 H3K27ac ChiP-seq in GI-ME-N ChiP-Atlas SRX8887748 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX7805843 GSM4340237 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX7805844 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX8806625 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX8806626 H3K27ac ChiP-seq in Jurkat ChiP-Atlas SRX2022917 H3K27ac ChiP-seq in Lymphoma B-cell ChiP-Atlas SRX4277998 H3K27ac ChiP-seq in Melanoma ChiP-Atlas SRX685325 GSM1484301 H3K27ac ChiP-seq in MUG-Chor1 ChiP-Atlas SRX3623423 H3K27ac ChiP-seq in PSC-derived hepatocyte-like ChiP-Atlas SRX12495361 H3K27ac ChiP-seq in PSC-derived hepatocyte-like ChiP-Atlas SRX12495362 H3K27ac ChiP-seq in T-All ChiP-Atlas SRX3216827 H3K4me1 ChiP-seq in ESC ChiP-Atlas SRX2881133 GSM2648927 H3K4me1 ChiP-seq in HepG2 ChiP-Atlas SRX3733792 H3K4me1 ChiP-seq in hESC-derived cardiac cell ChiP-Atlas SRX13466352 H3K4me1 ChiP-seq in IMR-90 ChiP-Atlas SRX119737 GSM873694 H3K4me1 ChiP-seq in iPSC ChiP-Atlas SRX8806628 H3K4me3 ChiP-seq in CD34+ ChiP-Atlas ERX690596 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299240 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299242 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299244 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299245 H3K4me3 ChiP-seq in iSLK ChiP-Atlas SRX503343 H3K4me3 ChiP-seq in neural progenitors ChiP-Atlas SRX8997967 Hi-C data of human cerebellum 28 ENCODE DCC-2017 (Continued on next page) 22 Cell Reports 45, 117146, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: cell lines Control iPS cell line GM23280 Coriell Institute Cat #GM23280 Control iPS cell line NAS6 gift from Dr T. Kunath, University of Edinburgh; Ludtmann et al.60 N/A Control iPS cell line ND41866 Coriell Institute Cat #ND41866 Fibroblast cell line AF2 Seixas et al.8 N/A Fibroblast cell line AF3 Seixas et al.8 N/A Fibroblast cell line AF4 Seixas et al.8 N/A Human embryonic kidney 293T (HEK293T) cell line ATCC Cat #CRL-3216 Human neural stem cells (hNCS) Sun et al.61 N/A SCA37 iPS cell line AF2Cl21 This study N/A SCA37 iPS cell line AF2Cl4 This study N/A SCA37 iPS cell line AF3Cl7 This study N/A SCA37 iPS cell line AF4Cl32 This study N/A Experimental models: organisms/strains Transgenic zebrafish line gSA2AzGFF152B; UAS:GFP Kindly gift by Drs. Kawakami and Hibi, Japan; Takeuchi et al.47; Asakawa et al.62 N/A Transgenic zebrafish line Tg(Frag1:EGFP) This study N/A Transgenic zebrafish line Tg(Frag3:EGFP) This study N/A Transgenic zebrafish line Tg(FragT:EGFP) This study N/A Zebrafish WTAB This study N/A Oligonucleotides Primers for 4C-seq are provided in Table S2 This study N/A Primers for cloning FragT and subfragments in pMCS or Topo8 are provided in Table S2 This study N/A Primers for cloning TK promoter in pGL4.23-GW are provided in Table S2 This study N/A Primers for genotyping of HEK293T cell clones are provided in Table S2 This study N/A Primers for qPCR are provided in Table S2 This study N/A SgRNAs used for FragT deletion are provided in Table S3 This study N/A Recombinant DNA
Recombinant:Article Title: Subversion of kynurenine-induced AHR activation in CD8 T cells by kynureninase-expressing antigen-presenting cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TMT 10-plex Thermo Scientific Cat# 90110 TMT 11-plex reagent (131C) Thermo Scientific Cat# A37724 Hydroxylamine Sigma-Aldrich Cat# 159417 Critical commercial assays Griess Reagent Kit Promega Cat# G2930 Lung Dissociation Kit Miltenyi Biotec Cat# 130-095-927 Dead Cell Removal Kit Miltenyi Biotec Cat# 130-090-101 PureLink RNA Mini Kit Invitrogen Cat# 12183025 SYBR Green Master Mix Miltenyi Biotec Cat# 130-052-301 gentleMACS Octo Dissociator Miltenyi Biotec Cat# 130-095-937 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 KAPA HotStart Mouse Genotyping Kit Sigma-Aldrich Cat# KK7351 Mouse Th1/Th2/Th17 Array Q1 RayBiotech Cat# QAM-TH17-1-1 Mouse IFN-gamma R1 DuoSet ELISA R&D systems Cat# DY1026 Deposited data Metabolomics LC MS raw data Mass Spectrometry Interactive Virtual Environment (MassIVE) (https://massive.ucsd.edu) MassIVE: MSV000100659 Mass spectrometry proteomics data https://www.proteomexchange.org/ ProteomeXchange: PXD074605 Experimental models: Cell lines TC1 Kromer lab N/A TC1IDO1 This paper N/A Experimental models: Organisms/strains Mouse: C57BL6/J (WT) Charles River Laboratory N/A Mouse: C57BL/6NJ-KYNUem1(IMPC)J/J (KYNUem1) The Jackson Laboratory N/A Mouse: B6.129-Ahrtm1Bra/J The Jackson Laboratory N/A Mouse: C57BL/6-Tg(TcraTcrb)1100Mjb/J The Jackson Laboratory N/A Oligonucleotides See Document S1 for mouse gene-specific primers used for qRT-PCR N/A Recombinant DNA pLJM1-EGFP Addgene Plasmid #19319 pLJM1-Ido1 This paper N/A Software and algorithms Image Lab (Version 6.1) Bio-Rad https://www.bio-rad.com/ Graphpad Prism 9 Graphpad https://www.graphpad.com/ Seahorse Wave Controller Software (version 2.4.2) Agilent https://www.agilent.com/ Compound Discoverer Thermo Fisher Scientific https://mycompounddiscoverer.com/ R Studio R https://www.rstudio.com/ Adobe Illustrator Adobe https://www.adobe.com Bio-Rad CFX Manager Bio-Rad https://www.bio-rad.com/ Maven Maven N/A Skyline MacCoss Lab Software https://skyline.ms/project/home/begin.view FCS Express 7 Flow Research Edition DeNovo Software https://denovosoftware.com/ BioRender BioRender https://biorender.com/ Sequest Thermo Fisher https://proteomicsresource.washington.edu/ protocols06/sequest.php Other QExactive Mass Spectrometer Thermo Fisher Scientific N/A (Continued on next page) 22 Cell Reports 45, 117149, April 28, 2026 .. C57BL6/J (WT) mice were obtained from Charles River Laboratories.
Article Title: SenCat: Cataloging human cell senescence through multi-omic profiling of multiple senescent primary cell types.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins DMEM Gibco Cat# 11965092 FBS Gibco Cat# A5256801 Penicillin-Streptomycin Gibco Cat# 15140122 Nonessential Amino Acids (100X) Gibco Cat# 11140050 Antibiotic-antimycotic (100X) Gibco Cat# 15240062 Maxima Reverse Transcriptase Thermo Scientific Cat# EP0743 KAPA SYBR Fast ABI Master Mix (2X) Roche Cat# 07959435001 RiboLock RNase Inhibitor Invitrogen Cat# EO0381 Random Primers Invitrogen Cat# 48190011 dNTP Mix (10 mM each) Thermo Scientific Cat# R0192 Sodium pyruvate Gibco 11360070 RPMI 1640 Gibco 11875093 Ham’s F-10 medium Gibco 11550043 Doxorubicin Selleckchem S1208 Etoposide Selleckchem S1225 Triethylammonium bicarbonate Thermo Fisher Scientific Cat# 90114 Dithiothreitol Sigma-Aldrich Cat# D9779 Iodoacetamide Sigma-Aldrich Cat# I1149 Trypsin Promega Cat# V5113 Formic acid Sigma-Aldrich Cat# 27001 Nonidet P40 Substitute Sigma-Aldrich Cat# 74385 Critical commercial assays RLT Buffer QIAGEN 79216 RNeasy Plus Mini Kit QIAGEN 74136 TruSeq Stranded Total RNA Library Prep Kit Illumina Cat# 20020598 AMPure XP beads Beckman Coulter Cat# A63881 SPRIselect beads Beckman Coulter Cat# B23318 BrdU Cell Proliferation Assay Kit Cell Signaling Technology Cat# 6813 Senescence β-Galactosidase Staining Kit Cell Signaling Technology Cat# 9860 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 Oasis HLB Solid Phase Extraction Cartridges Waters Cat# 186000383 Minute Single Nucleus Isolation Kit for Tissues/Cells Invent Biotechnologies Cat# SN-047 Chromium GEM-X Single Cell 3’ Kit v4 10x Genomics PN-1000691 Chromium Single Cell 3’ Library Construction Kit C 10x Genomics PN-1000694 Deposited data Previously published and/or public datasets used GEO ProteomeXchange GSE247719; PXD058684 Bulk RNA-seq data generated in this study GEO GSE285826 snRNA-seq data from doxorubicintreated mice GEO GSE302792 (Continued on next page) ll OPEN ACCESSResource Molecular Cell 86, 1–12.e1–e8, July 2, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bulk proteomic raw data MassIVE MSV000096215 Original microscopy images Mendeley Data DOI: 10.17632/5wt4tzhs7z.1 snRNA-seq refinement, senescence calling, and bulk proteomic analysis code Zenodo 10.5281/zenodo.19203645; 10.5281/ zenodo.19204600 ML analysis code Zenodo / GitHub DOI: 10.5281/zenodo.19333691; DOI: 10.
Plasmid Preparation:Article Title: Subversion of kynurenine-induced AHR activation in CD8 T cells by kynureninase-expressing antigen-presenting cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TMT 10-plex Thermo Scientific Cat# 90110 TMT 11-plex reagent (131C) Thermo Scientific Cat# A37724 Hydroxylamine Sigma-Aldrich Cat# 159417 Critical commercial assays Griess Reagent Kit Promega Cat# G2930 Lung Dissociation Kit Miltenyi Biotec Cat# 130-095-927 Dead Cell Removal Kit Miltenyi Biotec Cat# 130-090-101 PureLink RNA Mini Kit Invitrogen Cat# 12183025 SYBR Green Master Mix Miltenyi Biotec Cat# 130-052-301 gentleMACS Octo Dissociator Miltenyi Biotec Cat# 130-095-937 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 KAPA HotStart Mouse Genotyping Kit Sigma-Aldrich Cat# KK7351 Mouse Th1/Th2/Th17 Array Q1 RayBiotech Cat# QAM-TH17-1-1 Mouse IFN-gamma R1 DuoSet ELISA R&D systems Cat# DY1026 Deposited data Metabolomics LC MS raw data Mass Spectrometry Interactive Virtual Environment (MassIVE) (https://massive.ucsd.edu) MassIVE: MSV000100659 Mass spectrometry proteomics data https://www.proteomexchange.org/ ProteomeXchange: PXD074605 Experimental models: Cell lines TC1 Kromer lab N/A TC1IDO1 This paper N/A Experimental models: Organisms/strains Mouse: C57BL6/J (WT) Charles River Laboratory N/A Mouse: C57BL/6NJ-KYNUem1(IMPC)J/J (KYNUem1) The Jackson Laboratory N/A Mouse: B6.129-Ahrtm1Bra/J The Jackson Laboratory N/A Mouse: C57BL/6-Tg(TcraTcrb)1100Mjb/J The Jackson Laboratory N/A Oligonucleotides See Document S1 for mouse gene-specific primers used for qRT-PCR N/A Recombinant DNA pLJM1-EGFP Addgene Plasmid #19319 pLJM1-Ido1 This paper N/A Software and algorithms Image Lab (Version 6.1) Bio-Rad https://www.bio-rad.com/ Graphpad Prism 9 Graphpad https://www.graphpad.com/ Seahorse Wave Controller Software (version 2.4.2) Agilent https://www.agilent.com/ Compound Discoverer Thermo Fisher Scientific https://mycompounddiscoverer.com/ R Studio R https://www.rstudio.com/ Adobe Illustrator Adobe https://www.adobe.com Bio-Rad CFX Manager Bio-Rad https://www.bio-rad.com/ Maven Maven N/A Skyline MacCoss Lab Software https://skyline.ms/project/home/begin.view FCS Express 7 Flow Research Edition DeNovo Software https://denovosoftware.com/ BioRender BioRender https://biorender.com/ Sequest Thermo Fisher https://proteomicsresource.washington.edu/ protocols06/sequest.php Other QExactive Mass Spectrometer Thermo Fisher Scientific N/A (Continued on next page) 22 Cell Reports 45, 117149, April 28, 2026 .. C57BL6/J (WT) mice were obtained from Charles River Laboratories.
Software:Article Title: Subversion of kynurenine-induced AHR activation in CD8 T cells by kynureninase-expressing antigen-presenting cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TMT 10-plex Thermo Scientific Cat# 90110 TMT 11-plex reagent (131C) Thermo Scientific Cat# A37724 Hydroxylamine Sigma-Aldrich Cat# 159417 Critical commercial assays Griess Reagent Kit Promega Cat# G2930 Lung Dissociation Kit Miltenyi Biotec Cat# 130-095-927 Dead Cell Removal Kit Miltenyi Biotec Cat# 130-090-101 PureLink RNA Mini Kit Invitrogen Cat# 12183025 SYBR Green Master Mix Miltenyi Biotec Cat# 130-052-301 gentleMACS Octo Dissociator Miltenyi Biotec Cat# 130-095-937 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 KAPA HotStart Mouse Genotyping Kit Sigma-Aldrich Cat# KK7351 Mouse Th1/Th2/Th17 Array Q1 RayBiotech Cat# QAM-TH17-1-1 Mouse IFN-gamma R1 DuoSet ELISA R&D systems Cat# DY1026 Deposited data Metabolomics LC MS raw data Mass Spectrometry Interactive Virtual Environment (MassIVE) (https://massive.ucsd.edu) MassIVE: MSV000100659 Mass spectrometry proteomics data https://www.proteomexchange.org/ ProteomeXchange: PXD074605 Experimental models: Cell lines TC1 Kromer lab N/A TC1IDO1 This paper N/A Experimental models: Organisms/strains Mouse: C57BL6/J (WT) Charles River Laboratory N/A Mouse: C57BL/6NJ-KYNUem1(IMPC)J/J (KYNUem1) The Jackson Laboratory N/A Mouse: B6.129-Ahrtm1Bra/J The Jackson Laboratory N/A Mouse: C57BL/6-Tg(TcraTcrb)1100Mjb/J The Jackson Laboratory N/A Oligonucleotides See Document S1 for mouse gene-specific primers used for qRT-PCR N/A Recombinant DNA pLJM1-EGFP Addgene Plasmid #19319 pLJM1-Ido1 This paper N/A Software and algorithms Image Lab (Version 6.1) Bio-Rad https://www.bio-rad.com/ Graphpad Prism 9 Graphpad https://www.graphpad.com/ Seahorse Wave Controller Software (version 2.4.2) Agilent https://www.agilent.com/ Compound Discoverer Thermo Fisher Scientific https://mycompounddiscoverer.com/ R Studio R https://www.rstudio.com/ Adobe Illustrator Adobe https://www.adobe.com Bio-Rad CFX Manager Bio-Rad https://www.bio-rad.com/ Maven Maven N/A Skyline MacCoss Lab Software https://skyline.ms/project/home/begin.view FCS Express 7 Flow Research Edition DeNovo Software https://denovosoftware.com/ BioRender BioRender https://biorender.com/ Sequest Thermo Fisher https://proteomicsresource.washington.edu/ protocols06/sequest.php Other QExactive Mass Spectrometer Thermo Fisher Scientific N/A (Continued on next page) 22 Cell Reports 45, 117149, April 28, 2026 .. C57BL6/J (WT) mice were obtained from Charles River Laboratories.
Article Title: Circuit and molecular mechanisms underlying incubation of methamphetamine craving in the prelimbic cortex.
Article Snippet: Article Circuit and molecular mechanisms underlying incubation of methamphetamine craving in the prelimbic cortex Highlights • SST and PV interneurons in the PL differentially regulate methamphetamine craving • LHGABA → PLSST and AMGlu → PLPV circuits drive stagespecific craving • KCNC2 upregulation in interneurons underlies distinct neuronal excitability changes • Specific knockdown of KCNC2 reduces craving during early and prolonged withdrawal Authors Sai Shi, Yi-Wen Sun, Jin-Jun Ding, ..., Fang Liu, Ti-Fei Yuan, Min Zhao Correspondence fang.liu@camh.ca (F.L.), ytf0707@126.com (T..-F.Y.), drminzhao@smhc.org.cn (M.Z.). In brief Shi et al. reveal that two distinct interneurons in the PL control the incubation of methamphetamine craving during different withdrawal stages.. They uncover a circuit-switch principle and propose a key molecular mediator, offering phase-specific therapeutic strategies to reduce relapse.
Targeted Proteomics:Article Title: Subversion of kynurenine-induced AHR activation in CD8 T cells by kynureninase-expressing antigen-presenting cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TMT 10-plex Thermo Scientific Cat# 90110 TMT 11-plex reagent (131C) Thermo Scientific Cat# A37724 Hydroxylamine Sigma-Aldrich Cat# 159417 Critical commercial assays Griess Reagent Kit Promega Cat# G2930 Lung Dissociation Kit Miltenyi Biotec Cat# 130-095-927 Dead Cell Removal Kit Miltenyi Biotec Cat# 130-090-101 PureLink RNA Mini Kit Invitrogen Cat# 12183025 SYBR Green Master Mix Miltenyi Biotec Cat# 130-052-301 gentleMACS Octo Dissociator Miltenyi Biotec Cat# 130-095-937 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 KAPA HotStart Mouse Genotyping Kit Sigma-Aldrich Cat# KK7351 Mouse Th1/Th2/Th17 Array Q1 RayBiotech Cat# QAM-TH17-1-1 Mouse IFN-gamma R1 DuoSet ELISA R&D systems Cat# DY1026 Deposited data Metabolomics LC MS raw data Mass Spectrometry Interactive Virtual Environment (MassIVE) (https://massive.ucsd.edu) MassIVE: MSV000100659 Mass spectrometry proteomics data https://www.proteomexchange.org/ ProteomeXchange: PXD074605 Experimental models: Cell lines TC1 Kromer lab N/A TC1IDO1 This paper N/A Experimental models: Organisms/strains Mouse: C57BL6/J (WT) Charles River Laboratory N/A Mouse: C57BL/6NJ-KYNUem1(IMPC)J/J (KYNUem1) The Jackson Laboratory N/A Mouse: B6.129-Ahrtm1Bra/J The Jackson Laboratory N/A Mouse: C57BL/6-Tg(TcraTcrb)1100Mjb/J The Jackson Laboratory N/A Oligonucleotides See Document S1 for mouse gene-specific primers used for qRT-PCR N/A Recombinant DNA pLJM1-EGFP Addgene Plasmid #19319 pLJM1-Ido1 This paper N/A Software and algorithms Image Lab (Version 6.1) Bio-Rad https://www.bio-rad.com/ Graphpad Prism 9 Graphpad https://www.graphpad.com/ Seahorse Wave Controller Software (version 2.4.2) Agilent https://www.agilent.com/ Compound Discoverer Thermo Fisher Scientific https://mycompounddiscoverer.com/ R Studio R https://www.rstudio.com/ Adobe Illustrator Adobe https://www.adobe.com Bio-Rad CFX Manager Bio-Rad https://www.bio-rad.com/ Maven Maven N/A Skyline MacCoss Lab Software https://skyline.ms/project/home/begin.view FCS Express 7 Flow Research Edition DeNovo Software https://denovosoftware.com/ BioRender BioRender https://biorender.com/ Sequest Thermo Fisher https://proteomicsresource.washington.edu/ protocols06/sequest.php Other QExactive Mass Spectrometer Thermo Fisher Scientific N/A (Continued on next page) 22 Cell Reports 45, 117149, April 28, 2026 .. C57BL6/J (WT) mice were obtained from Charles River Laboratories.
Reporter Assay:Article Title: The insertion of an ATTTC repeat in an Alu element hyperactivates a neurodevelopmental enhancer in spinocerebellar ataxia type 37.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nano-Glo® Dual-Luciferase® Reporter Assay System Promega Cat #N1610 NZYMiniprep Kit NZYtech Cat #MB01002 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat #23227 PSC 4-Marker Immunocytochemistry Kit Thermo Fisher Scientific Cat #A24881 PureLinkTM RNA Micro Scale Kit Thermo Fisher Scientific Cat #12183016 QIAquick Gel Extraction Kit Zymoclean Gel DNA Recovery Kit QIAGEN Cat #28704 Quick-DNA Miniprep Kit ZYMO Research Cat #D4068S RNA Clean & Concentrator kit ZYMO Research Cat #R1017 RNeasy Mini Kit Qiagen Cat #74104 SuperScript III First-Strand Synthesis SuperMix for qRT-PCR Thermo Fisher Scientific Cat #11752050 Zymoclean Gel DNA Recovery Kit ZYMO Research Cat #D4008 Deposited data H3K27ac ChiP-seq in Acute myeloid leukemia ChiP-Atlas SRX13109961 H3K27ac ChiP-seq in CD4+ ChiP-Atlas SRX5944575 H3K27ac ChiP-seq in cerebellum ChiP-Atlas SRX5806022 GSM3755478 H3K27ac ChiP-seq in cerebellum ChiP-Atlas SRX263277 GSM1119154 H3K27ac ChiP-seq in GI-ME-N ChiP-Atlas SRX8887748 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX7805843 GSM4340237 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX7805844 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX8806625 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX8806626 H3K27ac ChiP-seq in Jurkat ChiP-Atlas SRX2022917 H3K27ac ChiP-seq in Lymphoma B-cell ChiP-Atlas SRX4277998 H3K27ac ChiP-seq in Melanoma ChiP-Atlas SRX685325 GSM1484301 H3K27ac ChiP-seq in MUG-Chor1 ChiP-Atlas SRX3623423 H3K27ac ChiP-seq in PSC-derived hepatocyte-like ChiP-Atlas SRX12495361 H3K27ac ChiP-seq in PSC-derived hepatocyte-like ChiP-Atlas SRX12495362 H3K27ac ChiP-seq in T-All ChiP-Atlas SRX3216827 H3K4me1 ChiP-seq in ESC ChiP-Atlas SRX2881133 GSM2648927 H3K4me1 ChiP-seq in HepG2 ChiP-Atlas SRX3733792 H3K4me1 ChiP-seq in hESC-derived cardiac cell ChiP-Atlas SRX13466352 H3K4me1 ChiP-seq in IMR-90 ChiP-Atlas SRX119737 GSM873694 H3K4me1 ChiP-seq in iPSC ChiP-Atlas SRX8806628 H3K4me3 ChiP-seq in CD34+ ChiP-Atlas ERX690596 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299240 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299242 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299244 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299245 H3K4me3 ChiP-seq in iSLK ChiP-Atlas SRX503343 H3K4me3 ChiP-seq in neural progenitors ChiP-Atlas SRX8997967 Hi-C data of human cerebellum 28 ENCODE DCC-2017 (Continued on next page) 22 Cell Reports 45, 117146, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: cell lines Control iPS cell line GM23280 Coriell Institute Cat #GM23280 Control iPS cell line NAS6 gift from Dr T. Kunath, University of Edinburgh; Ludtmann et al.60 N/A Control iPS cell line ND41866 Coriell Institute Cat #ND41866 Fibroblast cell line AF2 Seixas et al.8 N/A Fibroblast cell line AF3 Seixas et al.8 N/A Fibroblast cell line AF4 Seixas et al.8 N/A Human embryonic kidney 293T (HEK293T) cell line ATCC Cat #CRL-3216 Human neural stem cells (hNCS) Sun et al.61 N/A SCA37 iPS cell line AF2Cl21 This study N/A SCA37 iPS cell line AF2Cl4 This study N/A SCA37 iPS cell line AF3Cl7 This study N/A SCA37 iPS cell line AF4Cl32 This study N/A Experimental models: organisms/strains Transgenic zebrafish line gSA2AzGFF152B; UAS:GFP Kindly gift by Drs. Kawakami and Hibi, Japan; Takeuchi et al.47; Asakawa et al.62 N/A Transgenic zebrafish line Tg(Frag1:EGFP) This study N/A Transgenic zebrafish line Tg(Frag3:EGFP) This study N/A Transgenic zebrafish line Tg(FragT:EGFP) This study N/A Zebrafish WTAB This study N/A Oligonucleotides Primers for 4C-seq are provided in Table S2 This study N/A Primers for cloning FragT and subfragments in pMCS or Topo8 are provided in Table S2 This study N/A Primers for cloning TK promoter in pGL4.23-GW are provided in Table S2 This study N/A Primers for genotyping of HEK293T cell clones are provided in Table S2 This study N/A Primers for qPCR are provided in Table S2 This study N/A SgRNAs used for FragT deletion are provided in Table S3 This study N/A Recombinant DNA
Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Immunocytochemistry:Article Title: The insertion of an ATTTC repeat in an Alu element hyperactivates a neurodevelopmental enhancer in spinocerebellar ataxia type 37.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nano-Glo® Dual-Luciferase® Reporter Assay System Promega Cat #N1610 NZYMiniprep Kit NZYtech Cat #MB01002 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat #23227 PSC 4-Marker Immunocytochemistry Kit Thermo Fisher Scientific Cat #A24881 PureLinkTM RNA Micro Scale Kit Thermo Fisher Scientific Cat #12183016 QIAquick Gel Extraction Kit Zymoclean Gel DNA Recovery Kit QIAGEN Cat #28704 Quick-DNA Miniprep Kit ZYMO Research Cat #D4068S RNA Clean & Concentrator kit ZYMO Research Cat #R1017 RNeasy Mini Kit Qiagen Cat #74104 SuperScript III First-Strand Synthesis SuperMix for qRT-PCR Thermo Fisher Scientific Cat #11752050 Zymoclean Gel DNA Recovery Kit ZYMO Research Cat #D4008 Deposited data H3K27ac ChiP-seq in Acute myeloid leukemia ChiP-Atlas SRX13109961 H3K27ac ChiP-seq in CD4+ ChiP-Atlas SRX5944575 H3K27ac ChiP-seq in cerebellum ChiP-Atlas SRX5806022 GSM3755478 H3K27ac ChiP-seq in cerebellum ChiP-Atlas SRX263277 GSM1119154 H3K27ac ChiP-seq in GI-ME-N ChiP-Atlas SRX8887748 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX7805843 GSM4340237 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX7805844 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX8806625 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX8806626 H3K27ac ChiP-seq in Jurkat ChiP-Atlas SRX2022917 H3K27ac ChiP-seq in Lymphoma B-cell ChiP-Atlas SRX4277998 H3K27ac ChiP-seq in Melanoma ChiP-Atlas SRX685325 GSM1484301 H3K27ac ChiP-seq in MUG-Chor1 ChiP-Atlas SRX3623423 H3K27ac ChiP-seq in PSC-derived hepatocyte-like ChiP-Atlas SRX12495361 H3K27ac ChiP-seq in PSC-derived hepatocyte-like ChiP-Atlas SRX12495362 H3K27ac ChiP-seq in T-All ChiP-Atlas SRX3216827 H3K4me1 ChiP-seq in ESC ChiP-Atlas SRX2881133 GSM2648927 H3K4me1 ChiP-seq in HepG2 ChiP-Atlas SRX3733792 H3K4me1 ChiP-seq in hESC-derived cardiac cell ChiP-Atlas SRX13466352 H3K4me1 ChiP-seq in IMR-90 ChiP-Atlas SRX119737 GSM873694 H3K4me1 ChiP-seq in iPSC ChiP-Atlas SRX8806628 H3K4me3 ChiP-seq in CD34+ ChiP-Atlas ERX690596 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299240 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299242 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299244 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299245 H3K4me3 ChiP-seq in iSLK ChiP-Atlas SRX503343 H3K4me3 ChiP-seq in neural progenitors ChiP-Atlas SRX8997967 Hi-C data of human cerebellum 28 ENCODE DCC-2017 (Continued on next page) 22 Cell Reports 45, 117146, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: cell lines Control iPS cell line GM23280 Coriell Institute Cat #GM23280 Control iPS cell line NAS6 gift from Dr T. Kunath, University of Edinburgh; Ludtmann et al.60 N/A Control iPS cell line ND41866 Coriell Institute Cat #ND41866 Fibroblast cell line AF2 Seixas et al.8 N/A Fibroblast cell line AF3 Seixas et al.8 N/A Fibroblast cell line AF4 Seixas et al.8 N/A Human embryonic kidney 293T (HEK293T) cell line ATCC Cat #CRL-3216 Human neural stem cells (hNCS) Sun et al.61 N/A SCA37 iPS cell line AF2Cl21 This study N/A SCA37 iPS cell line AF2Cl4 This study N/A SCA37 iPS cell line AF3Cl7 This study N/A SCA37 iPS cell line AF4Cl32 This study N/A Experimental models: organisms/strains Transgenic zebrafish line gSA2AzGFF152B; UAS:GFP Kindly gift by Drs. Kawakami and Hibi, Japan; Takeuchi et al.47; Asakawa et al.62 N/A Transgenic zebrafish line Tg(Frag1:EGFP) This study N/A Transgenic zebrafish line Tg(Frag3:EGFP) This study N/A Transgenic zebrafish line Tg(FragT:EGFP) This study N/A Zebrafish WTAB This study N/A Oligonucleotides Primers for 4C-seq are provided in Table S2 This study N/A Primers for cloning FragT and subfragments in pMCS or Topo8 are provided in Table S2 This study N/A Primers for cloning TK promoter in pGL4.23-GW are provided in Table S2 This study N/A Primers for genotyping of HEK293T cell clones are provided in Table S2 This study N/A Primers for qPCR are provided in Table S2 This study N/A SgRNAs used for FragT deletion are provided in Table S3 This study N/A Recombinant DNA
Gel Extraction:Article Title: The insertion of an ATTTC repeat in an Alu element hyperactivates a neurodevelopmental enhancer in spinocerebellar ataxia type 37.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nano-Glo® Dual-Luciferase® Reporter Assay System Promega Cat #N1610 NZYMiniprep Kit NZYtech Cat #MB01002 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat #23227 PSC 4-Marker Immunocytochemistry Kit Thermo Fisher Scientific Cat #A24881 PureLinkTM RNA Micro Scale Kit Thermo Fisher Scientific Cat #12183016 QIAquick Gel Extraction Kit Zymoclean Gel DNA Recovery Kit QIAGEN Cat #28704 Quick-DNA Miniprep Kit ZYMO Research Cat #D4068S RNA Clean & Concentrator kit ZYMO Research Cat #R1017 RNeasy Mini Kit Qiagen Cat #74104 SuperScript III First-Strand Synthesis SuperMix for qRT-PCR Thermo Fisher Scientific Cat #11752050 Zymoclean Gel DNA Recovery Kit ZYMO Research Cat #D4008 Deposited data H3K27ac ChiP-seq in Acute myeloid leukemia ChiP-Atlas SRX13109961 H3K27ac ChiP-seq in CD4+ ChiP-Atlas SRX5944575 H3K27ac ChiP-seq in cerebellum ChiP-Atlas SRX5806022 GSM3755478 H3K27ac ChiP-seq in cerebellum ChiP-Atlas SRX263277 GSM1119154 H3K27ac ChiP-seq in GI-ME-N ChiP-Atlas SRX8887748 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX7805843 GSM4340237 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX7805844 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX8806625 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX8806626 H3K27ac ChiP-seq in Jurkat ChiP-Atlas SRX2022917 H3K27ac ChiP-seq in Lymphoma B-cell ChiP-Atlas SRX4277998 H3K27ac ChiP-seq in Melanoma ChiP-Atlas SRX685325 GSM1484301 H3K27ac ChiP-seq in MUG-Chor1 ChiP-Atlas SRX3623423 H3K27ac ChiP-seq in PSC-derived hepatocyte-like ChiP-Atlas SRX12495361 H3K27ac ChiP-seq in PSC-derived hepatocyte-like ChiP-Atlas SRX12495362 H3K27ac ChiP-seq in T-All ChiP-Atlas SRX3216827 H3K4me1 ChiP-seq in ESC ChiP-Atlas SRX2881133 GSM2648927 H3K4me1 ChiP-seq in HepG2 ChiP-Atlas SRX3733792 H3K4me1 ChiP-seq in hESC-derived cardiac cell ChiP-Atlas SRX13466352 H3K4me1 ChiP-seq in IMR-90 ChiP-Atlas SRX119737 GSM873694 H3K4me1 ChiP-seq in iPSC ChiP-Atlas SRX8806628 H3K4me3 ChiP-seq in CD34+ ChiP-Atlas ERX690596 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299240 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299242 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299244 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299245 H3K4me3 ChiP-seq in iSLK ChiP-Atlas SRX503343 H3K4me3 ChiP-seq in neural progenitors ChiP-Atlas SRX8997967 Hi-C data of human cerebellum 28 ENCODE DCC-2017 (Continued on next page) 22 Cell Reports 45, 117146, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: cell lines Control iPS cell line GM23280 Coriell Institute Cat #GM23280 Control iPS cell line NAS6 gift from Dr T. Kunath, University of Edinburgh; Ludtmann et al.60 N/A Control iPS cell line ND41866 Coriell Institute Cat #ND41866 Fibroblast cell line AF2 Seixas et al.8 N/A Fibroblast cell line AF3 Seixas et al.8 N/A Fibroblast cell line AF4 Seixas et al.8 N/A Human embryonic kidney 293T (HEK293T) cell line ATCC Cat #CRL-3216 Human neural stem cells (hNCS) Sun et al.61 N/A SCA37 iPS cell line AF2Cl21 This study N/A SCA37 iPS cell line AF2Cl4 This study N/A SCA37 iPS cell line AF3Cl7 This study N/A SCA37 iPS cell line AF4Cl32 This study N/A Experimental models: organisms/strains Transgenic zebrafish line gSA2AzGFF152B; UAS:GFP Kindly gift by Drs. Kawakami and Hibi, Japan; Takeuchi et al.47; Asakawa et al.62 N/A Transgenic zebrafish line Tg(Frag1:EGFP) This study N/A Transgenic zebrafish line Tg(Frag3:EGFP) This study N/A Transgenic zebrafish line Tg(FragT:EGFP) This study N/A Zebrafish WTAB This study N/A Oligonucleotides Primers for 4C-seq are provided in Table S2 This study N/A Primers for cloning FragT and subfragments in pMCS or Topo8 are provided in Table S2 This study N/A Primers for cloning TK promoter in pGL4.23-GW are provided in Table S2 This study N/A Primers for genotyping of HEK293T cell clones are provided in Table S2 This study N/A Primers for qPCR are provided in Table S2 This study N/A SgRNAs used for FragT deletion are provided in Table S3 This study N/A Recombinant DNA
Hi-C:Article Title: The insertion of an ATTTC repeat in an Alu element hyperactivates a neurodevelopmental enhancer in spinocerebellar ataxia type 37.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nano-Glo® Dual-Luciferase® Reporter Assay System Promega Cat #N1610 NZYMiniprep Kit NZYtech Cat #MB01002 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat #23227 PSC 4-Marker Immunocytochemistry Kit Thermo Fisher Scientific Cat #A24881 PureLinkTM RNA Micro Scale Kit Thermo Fisher Scientific Cat #12183016 QIAquick Gel Extraction Kit Zymoclean Gel DNA Recovery Kit QIAGEN Cat #28704 Quick-DNA Miniprep Kit ZYMO Research Cat #D4068S RNA Clean & Concentrator kit ZYMO Research Cat #R1017 RNeasy Mini Kit Qiagen Cat #74104 SuperScript III First-Strand Synthesis SuperMix for qRT-PCR Thermo Fisher Scientific Cat #11752050 Zymoclean Gel DNA Recovery Kit ZYMO Research Cat #D4008 Deposited data H3K27ac ChiP-seq in Acute myeloid leukemia ChiP-Atlas SRX13109961 H3K27ac ChiP-seq in CD4+ ChiP-Atlas SRX5944575 H3K27ac ChiP-seq in cerebellum ChiP-Atlas SRX5806022 GSM3755478 H3K27ac ChiP-seq in cerebellum ChiP-Atlas SRX263277 GSM1119154 H3K27ac ChiP-seq in GI-ME-N ChiP-Atlas SRX8887748 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX7805843 GSM4340237 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX7805844 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX8806625 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX8806626 H3K27ac ChiP-seq in Jurkat ChiP-Atlas SRX2022917 H3K27ac ChiP-seq in Lymphoma B-cell ChiP-Atlas SRX4277998 H3K27ac ChiP-seq in Melanoma ChiP-Atlas SRX685325 GSM1484301 H3K27ac ChiP-seq in MUG-Chor1 ChiP-Atlas SRX3623423 H3K27ac ChiP-seq in PSC-derived hepatocyte-like ChiP-Atlas SRX12495361 H3K27ac ChiP-seq in PSC-derived hepatocyte-like ChiP-Atlas SRX12495362 H3K27ac ChiP-seq in T-All ChiP-Atlas SRX3216827 H3K4me1 ChiP-seq in ESC ChiP-Atlas SRX2881133 GSM2648927 H3K4me1 ChiP-seq in HepG2 ChiP-Atlas SRX3733792 H3K4me1 ChiP-seq in hESC-derived cardiac cell ChiP-Atlas SRX13466352 H3K4me1 ChiP-seq in IMR-90 ChiP-Atlas SRX119737 GSM873694 H3K4me1 ChiP-seq in iPSC ChiP-Atlas SRX8806628 H3K4me3 ChiP-seq in CD34+ ChiP-Atlas ERX690596 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299240 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299242 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299244 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299245 H3K4me3 ChiP-seq in iSLK ChiP-Atlas SRX503343 H3K4me3 ChiP-seq in neural progenitors ChiP-Atlas SRX8997967 Hi-C data of human cerebellum 28 ENCODE DCC-2017 (Continued on next page) 22 Cell Reports 45, 117146, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: cell lines Control iPS cell line GM23280 Coriell Institute Cat #GM23280 Control iPS cell line NAS6 gift from Dr T. Kunath, University of Edinburgh; Ludtmann et al.60 N/A Control iPS cell line ND41866 Coriell Institute Cat #ND41866 Fibroblast cell line AF2 Seixas et al.8 N/A Fibroblast cell line AF3 Seixas et al.8 N/A Fibroblast cell line AF4 Seixas et al.8 N/A Human embryonic kidney 293T (HEK293T) cell line ATCC Cat #CRL-3216 Human neural stem cells (hNCS) Sun et al.61 N/A SCA37 iPS cell line AF2Cl21 This study N/A SCA37 iPS cell line AF2Cl4 This study N/A SCA37 iPS cell line AF3Cl7 This study N/A SCA37 iPS cell line AF4Cl32 This study N/A Experimental models: organisms/strains Transgenic zebrafish line gSA2AzGFF152B; UAS:GFP Kindly gift by Drs. Kawakami and Hibi, Japan; Takeuchi et al.47; Asakawa et al.62 N/A Transgenic zebrafish line Tg(Frag1:EGFP) This study N/A Transgenic zebrafish line Tg(Frag3:EGFP) This study N/A Transgenic zebrafish line Tg(FragT:EGFP) This study N/A Zebrafish WTAB This study N/A Oligonucleotides Primers for 4C-seq are provided in Table S2 This study N/A Primers for cloning FragT and subfragments in pMCS or Topo8 are provided in Table S2 This study N/A Primers for cloning TK promoter in pGL4.23-GW are provided in Table S2 This study N/A Primers for genotyping of HEK293T cell clones are provided in Table S2 This study N/A Primers for qPCR are provided in Table S2 This study N/A SgRNAs used for FragT deletion are provided in Table S3 This study N/A Recombinant DNA
Droplet Countercurrent Chromatography:Article Title: The insertion of an ATTTC repeat in an Alu element hyperactivates a neurodevelopmental enhancer in spinocerebellar ataxia type 37.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nano-Glo® Dual-Luciferase® Reporter Assay System Promega Cat #N1610 NZYMiniprep Kit NZYtech Cat #MB01002 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat #23227 PSC 4-Marker Immunocytochemistry Kit Thermo Fisher Scientific Cat #A24881 PureLinkTM RNA Micro Scale Kit Thermo Fisher Scientific Cat #12183016 QIAquick Gel Extraction Kit Zymoclean Gel DNA Recovery Kit QIAGEN Cat #28704 Quick-DNA Miniprep Kit ZYMO Research Cat #D4068S RNA Clean & Concentrator kit ZYMO Research Cat #R1017 RNeasy Mini Kit Qiagen Cat #74104 SuperScript III First-Strand Synthesis SuperMix for qRT-PCR Thermo Fisher Scientific Cat #11752050 Zymoclean Gel DNA Recovery Kit ZYMO Research Cat #D4008 Deposited data H3K27ac ChiP-seq in Acute myeloid leukemia ChiP-Atlas SRX13109961 H3K27ac ChiP-seq in CD4+ ChiP-Atlas SRX5944575 H3K27ac ChiP-seq in cerebellum ChiP-Atlas SRX5806022 GSM3755478 H3K27ac ChiP-seq in cerebellum ChiP-Atlas SRX263277 GSM1119154 H3K27ac ChiP-seq in GI-ME-N ChiP-Atlas SRX8887748 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX7805843 GSM4340237 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX7805844 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX8806625 H3K27ac ChiP-seq in iPSC ChiP-Atlas SRX8806626 H3K27ac ChiP-seq in Jurkat ChiP-Atlas SRX2022917 H3K27ac ChiP-seq in Lymphoma B-cell ChiP-Atlas SRX4277998 H3K27ac ChiP-seq in Melanoma ChiP-Atlas SRX685325 GSM1484301 H3K27ac ChiP-seq in MUG-Chor1 ChiP-Atlas SRX3623423 H3K27ac ChiP-seq in PSC-derived hepatocyte-like ChiP-Atlas SRX12495361 H3K27ac ChiP-seq in PSC-derived hepatocyte-like ChiP-Atlas SRX12495362 H3K27ac ChiP-seq in T-All ChiP-Atlas SRX3216827 H3K4me1 ChiP-seq in ESC ChiP-Atlas SRX2881133 GSM2648927 H3K4me1 ChiP-seq in HepG2 ChiP-Atlas SRX3733792 H3K4me1 ChiP-seq in hESC-derived cardiac cell ChiP-Atlas SRX13466352 H3K4me1 ChiP-seq in IMR-90 ChiP-Atlas SRX119737 GSM873694 H3K4me1 ChiP-seq in iPSC ChiP-Atlas SRX8806628 H3K4me3 ChiP-seq in CD34+ ChiP-Atlas ERX690596 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299240 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299242 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299244 H3K4me3 ChiP-seq in Glioma spheroid ChiP-Atlas SRX12299245 H3K4me3 ChiP-seq in iSLK ChiP-Atlas SRX503343 H3K4me3 ChiP-seq in neural progenitors ChiP-Atlas SRX8997967 Hi-C data of human cerebellum 28 ENCODE DCC-2017 (Continued on next page) 22 Cell Reports 45, 117146, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: cell lines Control iPS cell line GM23280 Coriell Institute Cat #GM23280 Control iPS cell line NAS6 gift from Dr T. Kunath, University of Edinburgh; Ludtmann et al.60 N/A Control iPS cell line ND41866 Coriell Institute Cat #ND41866 Fibroblast cell line AF2 Seixas et al.8 N/A Fibroblast cell line AF3 Seixas et al.8 N/A Fibroblast cell line AF4 Seixas et al.8 N/A Human embryonic kidney 293T (HEK293T) cell line ATCC Cat #CRL-3216 Human neural stem cells (hNCS) Sun et al.61 N/A SCA37 iPS cell line AF2Cl21 This study N/A SCA37 iPS cell line AF2Cl4 This study N/A SCA37 iPS cell line AF3Cl7 This study N/A SCA37 iPS cell line AF4Cl32 This study N/A Experimental models: organisms/strains Transgenic zebrafish line gSA2AzGFF152B; UAS:GFP Kindly gift by Drs. Kawakami and Hibi, Japan; Takeuchi et al.47; Asakawa et al.62 N/A Transgenic zebrafish line Tg(Frag1:EGFP) This study N/A Transgenic zebrafish line Tg(Frag3:EGFP) This study N/A Transgenic zebrafish line Tg(FragT:EGFP) This study N/A Zebrafish WTAB This study N/A Oligonucleotides Primers for 4C-seq are provided in Table S2 This study N/A Primers for cloning FragT and subfragments in pMCS or Topo8 are provided in Table S2 This study N/A Primers for cloning TK promoter in pGL4.23-GW are provided in Table S2 This study N/A Primers for genotyping of HEK293T cell clones are provided in Table S2 This study N/A Primers for qPCR are provided in Table S2 This study N/A SgRNAs used for FragT deletion are provided in Table S3 This study N/A Recombinant DNA
Reverse Transcription:Article Title: SenCat: Cataloging human cell senescence through multi-omic profiling of multiple senescent primary cell types.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins DMEM Gibco Cat# 11965092 FBS Gibco Cat# A5256801 Penicillin-Streptomycin Gibco Cat# 15140122 Nonessential Amino Acids (100X) Gibco Cat# 11140050 Antibiotic-antimycotic (100X) Gibco Cat# 15240062 Maxima Reverse Transcriptase Thermo Scientific Cat# EP0743 KAPA SYBR Fast ABI Master Mix (2X) Roche Cat# 07959435001 RiboLock RNase Inhibitor Invitrogen Cat# EO0381 Random Primers Invitrogen Cat# 48190011 dNTP Mix (10 mM each) Thermo Scientific Cat# R0192 Sodium pyruvate Gibco 11360070 RPMI 1640 Gibco 11875093 Ham’s F-10 medium Gibco 11550043 Doxorubicin Selleckchem S1208 Etoposide Selleckchem S1225 Triethylammonium bicarbonate Thermo Fisher Scientific Cat# 90114 Dithiothreitol Sigma-Aldrich Cat# D9779 Iodoacetamide Sigma-Aldrich Cat# I1149 Trypsin Promega Cat# V5113 Formic acid Sigma-Aldrich Cat# 27001 Nonidet P40 Substitute Sigma-Aldrich Cat# 74385 Critical commercial assays RLT Buffer QIAGEN 79216 RNeasy Plus Mini Kit QIAGEN 74136 TruSeq Stranded Total RNA Library Prep Kit Illumina Cat# 20020598 AMPure XP beads Beckman Coulter Cat# A63881 SPRIselect beads Beckman Coulter Cat# B23318 BrdU Cell Proliferation Assay Kit Cell Signaling Technology Cat# 6813 Senescence β-Galactosidase Staining Kit Cell Signaling Technology Cat# 9860 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 Oasis HLB Solid Phase Extraction Cartridges Waters Cat# 186000383 Minute Single Nucleus Isolation Kit for Tissues/Cells Invent Biotechnologies Cat# SN-047 Chromium GEM-X Single Cell 3’ Kit v4 10x Genomics PN-1000691 Chromium Single Cell 3’ Library Construction Kit C 10x Genomics PN-1000694 Deposited data Previously published and/or public datasets used GEO ProteomeXchange GSE247719; PXD058684 Bulk RNA-seq data generated in this study GEO GSE285826 snRNA-seq data from doxorubicintreated mice GEO GSE302792 (Continued on next page) ll OPEN ACCESSResource Molecular Cell 86, 1–12.e1–e8, July 2, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bulk proteomic raw data MassIVE MSV000096215 Original microscopy images Mendeley Data DOI: 10.17632/5wt4tzhs7z.1 snRNA-seq refinement, senescence calling, and bulk proteomic analysis code Zenodo 10.5281/zenodo.19203645; 10.5281/ zenodo.19204600 ML analysis code Zenodo / GitHub DOI: 10.5281/zenodo.19333691; DOI: 10.
Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
BrdU Cell Proliferation Assay:Article Title: SenCat: Cataloging human cell senescence through multi-omic profiling of multiple senescent primary cell types.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins DMEM Gibco Cat# 11965092 FBS Gibco Cat# A5256801 Penicillin-Streptomycin Gibco Cat# 15140122 Nonessential Amino Acids (100X) Gibco Cat# 11140050 Antibiotic-antimycotic (100X) Gibco Cat# 15240062 Maxima Reverse Transcriptase Thermo Scientific Cat# EP0743 KAPA SYBR Fast ABI Master Mix (2X) Roche Cat# 07959435001 RiboLock RNase Inhibitor Invitrogen Cat# EO0381 Random Primers Invitrogen Cat# 48190011 dNTP Mix (10 mM each) Thermo Scientific Cat# R0192 Sodium pyruvate Gibco 11360070 RPMI 1640 Gibco 11875093 Ham’s F-10 medium Gibco 11550043 Doxorubicin Selleckchem S1208 Etoposide Selleckchem S1225 Triethylammonium bicarbonate Thermo Fisher Scientific Cat# 90114 Dithiothreitol Sigma-Aldrich Cat# D9779 Iodoacetamide Sigma-Aldrich Cat# I1149 Trypsin Promega Cat# V5113 Formic acid Sigma-Aldrich Cat# 27001 Nonidet P40 Substitute Sigma-Aldrich Cat# 74385 Critical commercial assays RLT Buffer QIAGEN 79216 RNeasy Plus Mini Kit QIAGEN 74136 TruSeq Stranded Total RNA Library Prep Kit Illumina Cat# 20020598 AMPure XP beads Beckman Coulter Cat# A63881 SPRIselect beads Beckman Coulter Cat# B23318 BrdU Cell Proliferation Assay Kit Cell Signaling Technology Cat# 6813 Senescence β-Galactosidase Staining Kit Cell Signaling Technology Cat# 9860 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 Oasis HLB Solid Phase Extraction Cartridges Waters Cat# 186000383 Minute Single Nucleus Isolation Kit for Tissues/Cells Invent Biotechnologies Cat# SN-047 Chromium GEM-X Single Cell 3’ Kit v4 10x Genomics PN-1000691 Chromium Single Cell 3’ Library Construction Kit C 10x Genomics PN-1000694 Deposited data Previously published and/or public datasets used GEO ProteomeXchange GSE247719; PXD058684 Bulk RNA-seq data generated in this study GEO GSE285826 snRNA-seq data from doxorubicintreated mice GEO GSE302792 (Continued on next page) ll OPEN ACCESSResource Molecular Cell 86, 1–12.e1–e8, July 2, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bulk proteomic raw data MassIVE MSV000096215 Original microscopy images Mendeley Data DOI: 10.17632/5wt4tzhs7z.1 snRNA-seq refinement, senescence calling, and bulk proteomic analysis code Zenodo 10.5281/zenodo.19203645; 10.5281/ zenodo.19204600 ML analysis code Zenodo / GitHub DOI: 10.5281/zenodo.19333691; DOI: 10.
Staining:Article Title: SenCat: Cataloging human cell senescence through multi-omic profiling of multiple senescent primary cell types.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins DMEM Gibco Cat# 11965092 FBS Gibco Cat# A5256801 Penicillin-Streptomycin Gibco Cat# 15140122 Nonessential Amino Acids (100X) Gibco Cat# 11140050 Antibiotic-antimycotic (100X) Gibco Cat# 15240062 Maxima Reverse Transcriptase Thermo Scientific Cat# EP0743 KAPA SYBR Fast ABI Master Mix (2X) Roche Cat# 07959435001 RiboLock RNase Inhibitor Invitrogen Cat# EO0381 Random Primers Invitrogen Cat# 48190011 dNTP Mix (10 mM each) Thermo Scientific Cat# R0192 Sodium pyruvate Gibco 11360070 RPMI 1640 Gibco 11875093 Ham’s F-10 medium Gibco 11550043 Doxorubicin Selleckchem S1208 Etoposide Selleckchem S1225 Triethylammonium bicarbonate Thermo Fisher Scientific Cat# 90114 Dithiothreitol Sigma-Aldrich Cat# D9779 Iodoacetamide Sigma-Aldrich Cat# I1149 Trypsin Promega Cat# V5113 Formic acid Sigma-Aldrich Cat# 27001 Nonidet P40 Substitute Sigma-Aldrich Cat# 74385 Critical commercial assays RLT Buffer QIAGEN 79216 RNeasy Plus Mini Kit QIAGEN 74136 TruSeq Stranded Total RNA Library Prep Kit Illumina Cat# 20020598 AMPure XP beads Beckman Coulter Cat# A63881 SPRIselect beads Beckman Coulter Cat# B23318 BrdU Cell Proliferation Assay Kit Cell Signaling Technology Cat# 6813 Senescence β-Galactosidase Staining Kit Cell Signaling Technology Cat# 9860 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 Oasis HLB Solid Phase Extraction Cartridges Waters Cat# 186000383 Minute Single Nucleus Isolation Kit for Tissues/Cells Invent Biotechnologies Cat# SN-047 Chromium GEM-X Single Cell 3’ Kit v4 10x Genomics PN-1000691 Chromium Single Cell 3’ Library Construction Kit C 10x Genomics PN-1000694 Deposited data Previously published and/or public datasets used GEO ProteomeXchange GSE247719; PXD058684 Bulk RNA-seq data generated in this study GEO GSE285826 snRNA-seq data from doxorubicintreated mice GEO GSE302792 (Continued on next page) ll OPEN ACCESSResource Molecular Cell 86, 1–12.e1–e8, July 2, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bulk proteomic raw data MassIVE MSV000096215 Original microscopy images Mendeley Data DOI: 10.17632/5wt4tzhs7z.1 snRNA-seq refinement, senescence calling, and bulk proteomic analysis code Zenodo 10.5281/zenodo.19203645; 10.5281/ zenodo.19204600 ML analysis code Zenodo / GitHub DOI: 10.5281/zenodo.19333691; DOI: 10.
Extraction:Article Title: SenCat: Cataloging human cell senescence through multi-omic profiling of multiple senescent primary cell types.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins DMEM Gibco Cat# 11965092 FBS Gibco Cat# A5256801 Penicillin-Streptomycin Gibco Cat# 15140122 Nonessential Amino Acids (100X) Gibco Cat# 11140050 Antibiotic-antimycotic (100X) Gibco Cat# 15240062 Maxima Reverse Transcriptase Thermo Scientific Cat# EP0743 KAPA SYBR Fast ABI Master Mix (2X) Roche Cat# 07959435001 RiboLock RNase Inhibitor Invitrogen Cat# EO0381 Random Primers Invitrogen Cat# 48190011 dNTP Mix (10 mM each) Thermo Scientific Cat# R0192 Sodium pyruvate Gibco 11360070 RPMI 1640 Gibco 11875093 Ham’s F-10 medium Gibco 11550043 Doxorubicin Selleckchem S1208 Etoposide Selleckchem S1225 Triethylammonium bicarbonate Thermo Fisher Scientific Cat# 90114 Dithiothreitol Sigma-Aldrich Cat# D9779 Iodoacetamide Sigma-Aldrich Cat# I1149 Trypsin Promega Cat# V5113 Formic acid Sigma-Aldrich Cat# 27001 Nonidet P40 Substitute Sigma-Aldrich Cat# 74385 Critical commercial assays RLT Buffer QIAGEN 79216 RNeasy Plus Mini Kit QIAGEN 74136 TruSeq Stranded Total RNA Library Prep Kit Illumina Cat# 20020598 AMPure XP beads Beckman Coulter Cat# A63881 SPRIselect beads Beckman Coulter Cat# B23318 BrdU Cell Proliferation Assay Kit Cell Signaling Technology Cat# 6813 Senescence β-Galactosidase Staining Kit Cell Signaling Technology Cat# 9860 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 Oasis HLB Solid Phase Extraction Cartridges Waters Cat# 186000383 Minute Single Nucleus Isolation Kit for Tissues/Cells Invent Biotechnologies Cat# SN-047 Chromium GEM-X Single Cell 3’ Kit v4 10x Genomics PN-1000691 Chromium Single Cell 3’ Library Construction Kit C 10x Genomics PN-1000694 Deposited data Previously published and/or public datasets used GEO ProteomeXchange GSE247719; PXD058684 Bulk RNA-seq data generated in this study GEO GSE285826 snRNA-seq data from doxorubicintreated mice GEO GSE302792 (Continued on next page) ll OPEN ACCESSResource Molecular Cell 86, 1–12.e1–e8, July 2, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bulk proteomic raw data MassIVE MSV000096215 Original microscopy images Mendeley Data DOI: 10.17632/5wt4tzhs7z.1 snRNA-seq refinement, senescence calling, and bulk proteomic analysis code Zenodo 10.5281/zenodo.19203645; 10.5281/ zenodo.19204600 ML analysis code Zenodo / GitHub DOI: 10.5281/zenodo.19333691; DOI: 10.
Isolation:Article Title: SenCat: Cataloging human cell senescence through multi-omic profiling of multiple senescent primary cell types.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins DMEM Gibco Cat# 11965092 FBS Gibco Cat# A5256801 Penicillin-Streptomycin Gibco Cat# 15140122 Nonessential Amino Acids (100X) Gibco Cat# 11140050 Antibiotic-antimycotic (100X) Gibco Cat# 15240062 Maxima Reverse Transcriptase Thermo Scientific Cat# EP0743 KAPA SYBR Fast ABI Master Mix (2X) Roche Cat# 07959435001 RiboLock RNase Inhibitor Invitrogen Cat# EO0381 Random Primers Invitrogen Cat# 48190011 dNTP Mix (10 mM each) Thermo Scientific Cat# R0192 Sodium pyruvate Gibco 11360070 RPMI 1640 Gibco 11875093 Ham’s F-10 medium Gibco 11550043 Doxorubicin Selleckchem S1208 Etoposide Selleckchem S1225 Triethylammonium bicarbonate Thermo Fisher Scientific Cat# 90114 Dithiothreitol Sigma-Aldrich Cat# D9779 Iodoacetamide Sigma-Aldrich Cat# I1149 Trypsin Promega Cat# V5113 Formic acid Sigma-Aldrich Cat# 27001 Nonidet P40 Substitute Sigma-Aldrich Cat# 74385 Critical commercial assays RLT Buffer QIAGEN 79216 RNeasy Plus Mini Kit QIAGEN 74136 TruSeq Stranded Total RNA Library Prep Kit Illumina Cat# 20020598 AMPure XP beads Beckman Coulter Cat# A63881 SPRIselect beads Beckman Coulter Cat# B23318 BrdU Cell Proliferation Assay Kit Cell Signaling Technology Cat# 6813 Senescence β-Galactosidase Staining Kit Cell Signaling Technology Cat# 9860 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 Oasis HLB Solid Phase Extraction Cartridges Waters Cat# 186000383 Minute Single Nucleus Isolation Kit for Tissues/Cells Invent Biotechnologies Cat# SN-047 Chromium GEM-X Single Cell 3’ Kit v4 10x Genomics PN-1000691 Chromium Single Cell 3’ Library Construction Kit C 10x Genomics PN-1000694 Deposited data Previously published and/or public datasets used GEO ProteomeXchange GSE247719; PXD058684 Bulk RNA-seq data generated in this study GEO GSE285826 snRNA-seq data from doxorubicintreated mice GEO GSE302792 (Continued on next page) ll OPEN ACCESSResource Molecular Cell 86, 1–12.e1–e8, July 2, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bulk proteomic raw data MassIVE MSV000096215 Original microscopy images Mendeley Data DOI: 10.17632/5wt4tzhs7z.1 snRNA-seq refinement, senescence calling, and bulk proteomic analysis code Zenodo 10.5281/zenodo.19203645; 10.5281/ zenodo.19204600 ML analysis code Zenodo / GitHub DOI: 10.5281/zenodo.19333691; DOI: 10.
Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Single Cell:Article Title: SenCat: Cataloging human cell senescence through multi-omic profiling of multiple senescent primary cell types.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins DMEM Gibco Cat# 11965092 FBS Gibco Cat# A5256801 Penicillin-Streptomycin Gibco Cat# 15140122 Nonessential Amino Acids (100X) Gibco Cat# 11140050 Antibiotic-antimycotic (100X) Gibco Cat# 15240062 Maxima Reverse Transcriptase Thermo Scientific Cat# EP0743 KAPA SYBR Fast ABI Master Mix (2X) Roche Cat# 07959435001 RiboLock RNase Inhibitor Invitrogen Cat# EO0381 Random Primers Invitrogen Cat# 48190011 dNTP Mix (10 mM each) Thermo Scientific Cat# R0192 Sodium pyruvate Gibco 11360070 RPMI 1640 Gibco 11875093 Ham’s F-10 medium Gibco 11550043 Doxorubicin Selleckchem S1208 Etoposide Selleckchem S1225 Triethylammonium bicarbonate Thermo Fisher Scientific Cat# 90114 Dithiothreitol Sigma-Aldrich Cat# D9779 Iodoacetamide Sigma-Aldrich Cat# I1149 Trypsin Promega Cat# V5113 Formic acid Sigma-Aldrich Cat# 27001 Nonidet P40 Substitute Sigma-Aldrich Cat# 74385 Critical commercial assays RLT Buffer QIAGEN 79216 RNeasy Plus Mini Kit QIAGEN 74136 TruSeq Stranded Total RNA Library Prep Kit Illumina Cat# 20020598 AMPure XP beads Beckman Coulter Cat# A63881 SPRIselect beads Beckman Coulter Cat# B23318 BrdU Cell Proliferation Assay Kit Cell Signaling Technology Cat# 6813 Senescence β-Galactosidase Staining Kit Cell Signaling Technology Cat# 9860 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 Oasis HLB Solid Phase Extraction Cartridges Waters Cat# 186000383 Minute Single Nucleus Isolation Kit for Tissues/Cells Invent Biotechnologies Cat# SN-047 Chromium GEM-X Single Cell 3’ Kit v4 10x Genomics PN-1000691 Chromium Single Cell 3’ Library Construction Kit C 10x Genomics PN-1000694 Deposited data Previously published and/or public datasets used GEO ProteomeXchange GSE247719; PXD058684 Bulk RNA-seq data generated in this study GEO GSE285826 snRNA-seq data from doxorubicintreated mice GEO GSE302792 (Continued on next page) ll OPEN ACCESSResource Molecular Cell 86, 1–12.e1–e8, July 2, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bulk proteomic raw data MassIVE MSV000096215 Original microscopy images Mendeley Data DOI: 10.17632/5wt4tzhs7z.1 snRNA-seq refinement, senescence calling, and bulk proteomic analysis code Zenodo 10.5281/zenodo.19203645; 10.5281/ zenodo.19204600 ML analysis code Zenodo / GitHub DOI: 10.5281/zenodo.19333691; DOI: 10.
RNA Sequencing:Article Title: SenCat: Cataloging human cell senescence through multi-omic profiling of multiple senescent primary cell types.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins DMEM Gibco Cat# 11965092 FBS Gibco Cat# A5256801 Penicillin-Streptomycin Gibco Cat# 15140122 Nonessential Amino Acids (100X) Gibco Cat# 11140050 Antibiotic-antimycotic (100X) Gibco Cat# 15240062 Maxima Reverse Transcriptase Thermo Scientific Cat# EP0743 KAPA SYBR Fast ABI Master Mix (2X) Roche Cat# 07959435001 RiboLock RNase Inhibitor Invitrogen Cat# EO0381 Random Primers Invitrogen Cat# 48190011 dNTP Mix (10 mM each) Thermo Scientific Cat# R0192 Sodium pyruvate Gibco 11360070 RPMI 1640 Gibco 11875093 Ham’s F-10 medium Gibco 11550043 Doxorubicin Selleckchem S1208 Etoposide Selleckchem S1225 Triethylammonium bicarbonate Thermo Fisher Scientific Cat# 90114 Dithiothreitol Sigma-Aldrich Cat# D9779 Iodoacetamide Sigma-Aldrich Cat# I1149 Trypsin Promega Cat# V5113 Formic acid Sigma-Aldrich Cat# 27001 Nonidet P40 Substitute Sigma-Aldrich Cat# 74385 Critical commercial assays RLT Buffer QIAGEN 79216 RNeasy Plus Mini Kit QIAGEN 74136 TruSeq Stranded Total RNA Library Prep Kit Illumina Cat# 20020598 AMPure XP beads Beckman Coulter Cat# A63881 SPRIselect beads Beckman Coulter Cat# B23318 BrdU Cell Proliferation Assay Kit Cell Signaling Technology Cat# 6813 Senescence β-Galactosidase Staining Kit Cell Signaling Technology Cat# 9860 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 Oasis HLB Solid Phase Extraction Cartridges Waters Cat# 186000383 Minute Single Nucleus Isolation Kit for Tissues/Cells Invent Biotechnologies Cat# SN-047 Chromium GEM-X Single Cell 3’ Kit v4 10x Genomics PN-1000691 Chromium Single Cell 3’ Library Construction Kit C 10x Genomics PN-1000694 Deposited data Previously published and/or public datasets used GEO ProteomeXchange GSE247719; PXD058684 Bulk RNA-seq data generated in this study GEO GSE285826 snRNA-seq data from doxorubicintreated mice GEO GSE302792 (Continued on next page) ll OPEN ACCESSResource Molecular Cell 86, 1–12.e1–e8, July 2, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bulk proteomic raw data MassIVE MSV000096215 Original microscopy images Mendeley Data DOI: 10.17632/5wt4tzhs7z.1 snRNA-seq refinement, senescence calling, and bulk proteomic analysis code Zenodo 10.5281/zenodo.19203645; 10.5281/ zenodo.19204600 ML analysis code Zenodo / GitHub DOI: 10.5281/zenodo.19333691; DOI: 10.
Article Title: A human iPSC-derived sensory neuron platform for high-throughput discovery of neuroprotectants against chemotherapy-induced peripheral neuropathy.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER LIVE/DEAD far-red dye (LDR) Thermo Fisher Scientific Cat# L10120 Critical commercial assays Caspase-Glo® 3/7 Assay System Promega Cat# G8090 Pierce High-Select FeNTA Phosphopeptide Enrichment Kit Thermo Scientific Cat# A32992 MACS Embryoid Body Dissociation Kit Miltenyi Biotech Cat# 130-096-348 BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23235 Deposited data Bulk RNA Sequencing Data This paper GEO: GSE298389 Proteomic and Phosphoproteomic Data This paper ProteomeXchange Consortium via PRIDE (ID: PXD074954). .. Experimental models: Cell lines Human iPSC line LiPSC.GR-1.1 (male donor) NIH Common Fund (Regenerative Medicine Program) N/A Primary human DRG neurons AnaBios Corporation N/A iCell Sensory Neurons, Female FUJIFILM Cat# 21527 iCell Sensory Neurons, Male FUJIFILM Cat# 01279 MCF7 breast cancer cells ATCC HTB-22 BT20 breast cancer cells ATCC HTB-19 BT549 breast cancer cells ATCC HTB-122 Hs578 T breast cancer cells ATCC HTB-126 ReN VM neural progenitor cells EMD Millipore SCC008 Experimental models: Organisms/strains Mouse: A/J (Strain 646) Jackson Laboratory 000646 Oligonucleotides siRNA against MAP4K6 (MINK1) Thermo Fisher Scientific Cat# s27006 siRNA against MAP4K7 (TNIK) Thermo Fisher Scientific Cat# s22905 siRNA against MAP4K4 (HGK) Thermo Fisher Scientific Cat# s18096 Software and algorithms Custom Analysis Code This paper https://github.com/labsyspharm/ peripheral-neuropathy MetaXpress Custom Module Editor Molecular Devices RRID: SCR_016654 IncuCyte Sartorius RRID: SCR_025411 GraphPad Prism GraphPad RRID: SCR_002798 Seaborn (Python) https://doi.org/10.21105/joss.03021 RRID: SCR_018132 fgsea v1.32.4 https://doi.org/10.1101/060012 RRID: SCR_020938 DESeq2 v1.46.0 https://doi.org/10.1186/s13059-014-0550-8 RRID: SCR_015687 limma v3.62.2 https://doi.org/10.1093/nar/gkv007 RRID: SCR_010943 Salmon v1.10.3 https://doi.org/10.1038/nmeth.4197 RRID: SCR_017036 tximport v1.34.0 https://doi.org/10.12688/f1000research.7563.1 RRID: SCR_016752 msigdbr v24.1.0 https://doi.org/10.1016/J.CELS.2015.12.004 RRID: SCR_022870 R v4.4.2 R project RRID: SCR_001905 Cell Reports Medicine 7, 102787, May 19, 2026 e2 Article ll OPEN ACCESS plates at 37◦C and 5% CO2.
Generated:Article Title: SenCat: Cataloging human cell senescence through multi-omic profiling of multiple senescent primary cell types.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins DMEM Gibco Cat# 11965092 FBS Gibco Cat# A5256801 Penicillin-Streptomycin Gibco Cat# 15140122 Nonessential Amino Acids (100X) Gibco Cat# 11140050 Antibiotic-antimycotic (100X) Gibco Cat# 15240062 Maxima Reverse Transcriptase Thermo Scientific Cat# EP0743 KAPA SYBR Fast ABI Master Mix (2X) Roche Cat# 07959435001 RiboLock RNase Inhibitor Invitrogen Cat# EO0381 Random Primers Invitrogen Cat# 48190011 dNTP Mix (10 mM each) Thermo Scientific Cat# R0192 Sodium pyruvate Gibco 11360070 RPMI 1640 Gibco 11875093 Ham’s F-10 medium Gibco 11550043 Doxorubicin Selleckchem S1208 Etoposide Selleckchem S1225 Triethylammonium bicarbonate Thermo Fisher Scientific Cat# 90114 Dithiothreitol Sigma-Aldrich Cat# D9779 Iodoacetamide Sigma-Aldrich Cat# I1149 Trypsin Promega Cat# V5113 Formic acid Sigma-Aldrich Cat# 27001 Nonidet P40 Substitute Sigma-Aldrich Cat# 74385 Critical commercial assays RLT Buffer QIAGEN 79216 RNeasy Plus Mini Kit QIAGEN 74136 TruSeq Stranded Total RNA Library Prep Kit Illumina Cat# 20020598 AMPure XP beads Beckman Coulter Cat# A63881 SPRIselect beads Beckman Coulter Cat# B23318 BrdU Cell Proliferation Assay Kit Cell Signaling Technology Cat# 6813 Senescence β-Galactosidase Staining Kit Cell Signaling Technology Cat# 9860 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23225 Oasis HLB Solid Phase Extraction Cartridges Waters Cat# 186000383 Minute Single Nucleus Isolation Kit for Tissues/Cells Invent Biotechnologies Cat# SN-047 Chromium GEM-X Single Cell 3’ Kit v4 10x Genomics PN-1000691 Chromium Single Cell 3’ Library Construction Kit C 10x Genomics PN-1000694 Deposited data Previously published and/or public datasets used GEO ProteomeXchange GSE247719; PXD058684 Bulk RNA-seq data generated in this study GEO GSE285826 snRNA-seq data from doxorubicintreated mice GEO GSE302792 (Continued on next page) ll OPEN ACCESSResource Molecular Cell 86, 1–12.e1–e8, July 2, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bulk proteomic raw data MassIVE MSV000096215 Original microscopy images Mendeley Data DOI: 10.17632/5wt4tzhs7z.1 snRNA-seq refinement, senescence calling, and bulk proteomic analysis code Zenodo 10.5281/zenodo.19203645; 10.5281/ zenodo.19204600 ML analysis code Zenodo / GitHub DOI: 10.5281/zenodo.19333691; DOI: 10.
Caspase-Glo Assay:Article Title: A human iPSC-derived sensory neuron platform for high-throughput discovery of neuroprotectants against chemotherapy-induced peripheral neuropathy.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER LIVE/DEAD far-red dye (LDR) Thermo Fisher Scientific Cat# L10120 Critical commercial assays Caspase-Glo® 3/7 Assay System Promega Cat# G8090 Pierce High-Select FeNTA Phosphopeptide Enrichment Kit Thermo Scientific Cat# A32992 MACS Embryoid Body Dissociation Kit Miltenyi Biotech Cat# 130-096-348 BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23235 Deposited data Bulk RNA Sequencing Data This paper GEO: GSE298389 Proteomic and Phosphoproteomic Data This paper ProteomeXchange Consortium via PRIDE (ID: PXD074954). .. Experimental models: Cell lines Human iPSC line LiPSC.GR-1.1 (male donor) NIH Common Fund (Regenerative Medicine Program) N/A Primary human DRG neurons AnaBios Corporation N/A iCell Sensory Neurons, Female FUJIFILM Cat# 21527 iCell Sensory Neurons, Male FUJIFILM Cat# 01279 MCF7 breast cancer cells ATCC HTB-22 BT20 breast cancer cells ATCC HTB-19 BT549 breast cancer cells ATCC HTB-122 Hs578 T breast cancer cells ATCC HTB-126 ReN VM neural progenitor cells EMD Millipore SCC008 Experimental models: Organisms/strains Mouse: A/J (Strain 646) Jackson Laboratory 000646 Oligonucleotides siRNA against MAP4K6 (MINK1) Thermo Fisher Scientific Cat# s27006 siRNA against MAP4K7 (TNIK) Thermo Fisher Scientific Cat# s22905 siRNA against MAP4K4 (HGK) Thermo Fisher Scientific Cat# s18096 Software and algorithms Custom Analysis Code This paper https://github.com/labsyspharm/ peripheral-neuropathy MetaXpress Custom Module Editor Molecular Devices RRID: SCR_016654 IncuCyte Sartorius RRID: SCR_025411 GraphPad Prism GraphPad RRID: SCR_002798 Seaborn (Python) https://doi.org/10.21105/joss.03021 RRID: SCR_018132 fgsea v1.32.4 https://doi.org/10.1101/060012 RRID: SCR_020938 DESeq2 v1.46.0 https://doi.org/10.1186/s13059-014-0550-8 RRID: SCR_015687 limma v3.62.2 https://doi.org/10.1093/nar/gkv007 RRID: SCR_010943 Salmon v1.10.3 https://doi.org/10.1038/nmeth.4197 RRID: SCR_017036 tximport v1.34.0 https://doi.org/10.12688/f1000research.7563.1 RRID: SCR_016752 msigdbr v24.1.0 https://doi.org/10.1016/J.CELS.2015.12.004 RRID: SCR_022870 R v4.4.2 R project RRID: SCR_001905 Cell Reports Medicine 7, 102787, May 19, 2026 e2 Article ll OPEN ACCESS plates at 37◦C and 5% CO2.
Phospho-proteomics:Article Title: A human iPSC-derived sensory neuron platform for high-throughput discovery of neuroprotectants against chemotherapy-induced peripheral neuropathy.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER LIVE/DEAD far-red dye (LDR) Thermo Fisher Scientific Cat# L10120 Critical commercial assays Caspase-Glo® 3/7 Assay System Promega Cat# G8090 Pierce High-Select FeNTA Phosphopeptide Enrichment Kit Thermo Scientific Cat# A32992 MACS Embryoid Body Dissociation Kit Miltenyi Biotech Cat# 130-096-348 BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23235 Deposited data Bulk RNA Sequencing Data This paper GEO: GSE298389 Proteomic and Phosphoproteomic Data This paper ProteomeXchange Consortium via PRIDE (ID: PXD074954). .. Experimental models: Cell lines Human iPSC line LiPSC.GR-1.1 (male donor) NIH Common Fund (Regenerative Medicine Program) N/A Primary human DRG neurons AnaBios Corporation N/A iCell Sensory Neurons, Female FUJIFILM Cat# 21527 iCell Sensory Neurons, Male FUJIFILM Cat# 01279 MCF7 breast cancer cells ATCC HTB-22 BT20 breast cancer cells ATCC HTB-19 BT549 breast cancer cells ATCC HTB-122 Hs578 T breast cancer cells ATCC HTB-126 ReN VM neural progenitor cells EMD Millipore SCC008 Experimental models: Organisms/strains Mouse: A/J (Strain 646) Jackson Laboratory 000646 Oligonucleotides siRNA against MAP4K6 (MINK1) Thermo Fisher Scientific Cat# s27006 siRNA against MAP4K7 (TNIK) Thermo Fisher Scientific Cat# s22905 siRNA against MAP4K4 (HGK) Thermo Fisher Scientific Cat# s18096 Software and algorithms Custom Analysis Code This paper https://github.com/labsyspharm/ peripheral-neuropathy MetaXpress Custom Module Editor Molecular Devices RRID: SCR_016654 IncuCyte Sartorius RRID: SCR_025411 GraphPad Prism GraphPad RRID: SCR_002798 Seaborn (Python) https://doi.org/10.21105/joss.03021 RRID: SCR_018132 fgsea v1.32.4 https://doi.org/10.1101/060012 RRID: SCR_020938 DESeq2 v1.46.0 https://doi.org/10.1186/s13059-014-0550-8 RRID: SCR_015687 limma v3.62.2 https://doi.org/10.1093/nar/gkv007 RRID: SCR_010943 Salmon v1.10.3 https://doi.org/10.1038/nmeth.4197 RRID: SCR_017036 tximport v1.34.0 https://doi.org/10.12688/f1000research.7563.1 RRID: SCR_016752 msigdbr v24.1.0 https://doi.org/10.1016/J.CELS.2015.12.004 RRID: SCR_022870 R v4.4.2 R project RRID: SCR_001905 Cell Reports Medicine 7, 102787, May 19, 2026 e2 Article ll OPEN ACCESS plates at 37◦C and 5% CO2.
Magnetic Cell Separation:Article Title: A human iPSC-derived sensory neuron platform for high-throughput discovery of neuroprotectants against chemotherapy-induced peripheral neuropathy.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER LIVE/DEAD far-red dye (LDR) Thermo Fisher Scientific Cat# L10120 Critical commercial assays Caspase-Glo® 3/7 Assay System Promega Cat# G8090 Pierce High-Select FeNTA Phosphopeptide Enrichment Kit Thermo Scientific Cat# A32992 MACS Embryoid Body Dissociation Kit Miltenyi Biotech Cat# 130-096-348 BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23235 Deposited data Bulk RNA Sequencing Data This paper GEO: GSE298389 Proteomic and Phosphoproteomic Data This paper ProteomeXchange Consortium via PRIDE (ID: PXD074954). .. Experimental models: Cell lines Human iPSC line LiPSC.GR-1.1 (male donor) NIH Common Fund (Regenerative Medicine Program) N/A Primary human DRG neurons AnaBios Corporation N/A iCell Sensory Neurons, Female FUJIFILM Cat# 21527 iCell Sensory Neurons, Male FUJIFILM Cat# 01279 MCF7 breast cancer cells ATCC HTB-22 BT20 breast cancer cells ATCC HTB-19 BT549 breast cancer cells ATCC HTB-122 Hs578 T breast cancer cells ATCC HTB-126 ReN VM neural progenitor cells EMD Millipore SCC008 Experimental models: Organisms/strains Mouse: A/J (Strain 646) Jackson Laboratory 000646 Oligonucleotides siRNA against MAP4K6 (MINK1) Thermo Fisher Scientific Cat# s27006 siRNA against MAP4K7 (TNIK) Thermo Fisher Scientific Cat# s22905 siRNA against MAP4K4 (HGK) Thermo Fisher Scientific Cat# s18096 Software and algorithms Custom Analysis Code This paper https://github.com/labsyspharm/ peripheral-neuropathy MetaXpress Custom Module Editor Molecular Devices RRID: SCR_016654 IncuCyte Sartorius RRID: SCR_025411 GraphPad Prism GraphPad RRID: SCR_002798 Seaborn (Python) https://doi.org/10.21105/joss.03021 RRID: SCR_018132 fgsea v1.32.4 https://doi.org/10.1101/060012 RRID: SCR_020938 DESeq2 v1.46.0 https://doi.org/10.1186/s13059-014-0550-8 RRID: SCR_015687 limma v3.62.2 https://doi.org/10.1093/nar/gkv007 RRID: SCR_010943 Salmon v1.10.3 https://doi.org/10.1038/nmeth.4197 RRID: SCR_017036 tximport v1.34.0 https://doi.org/10.12688/f1000research.7563.1 RRID: SCR_016752 msigdbr v24.1.0 https://doi.org/10.1016/J.CELS.2015.12.004 RRID: SCR_022870 R v4.4.2 R project RRID: SCR_001905 Cell Reports Medicine 7, 102787, May 19, 2026 e2 Article ll OPEN ACCESS plates at 37◦C and 5% CO2.
other:Article Title: Iron drives protease-independent cleavage of gasdermin D in allergic airway diseases.
Article Snippet: Article Iron drives protease-independent cleavage of gasdermin D in allergic airway diseases
Article Title: Heat shock protein 90β lactylation acts as a metabolic switch to drive cerebrovascular apoptosis under heat stress.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-β-Actin antibody Proteintech Cat# 60008-1-Ig; RRID: AB_2289225 Anti-P53 antibody Proteintech Cat# 60283-2-Ig; RRID: AB_2881401 Anti-Bcl2 antibody Proteintech Cat# 26593-1-AP; RRID: AB_2818996 Anti-Bax antibody Proteintech Cat# 60267-1-Ig; RRID: AB_2848213 Anti-Cleaved-Caspase3 antibody Proteintech Cat# 25128-1-AP; RRID: AB_3073913 Anti-HSP90 antibody BOSTER Cat# BM4387; RRID: AB_3741811 Anti-HSP90β antibody Proteintech Cat# 67450-1-Ig; RRID: AB_2882684-1-Ig Pan-Kla monoclonal antibody PTM BioLab Cat# PTM-1401; RRID: AB_2868521 Anti-HSP90β K275la antibody PTM BioLab Custom antibody; RRID: AB_3750172 Anti-CD31 antibody Proteintech Cat# 28083-1-AP; RRID: AB_2881055 Anti-ZO-1 antibody Proteintech Cat# 21773-1-AP; RRID: AB_1073324 Chemicals, peptides, and recombinant proteins DMEM Gbico Cat# C11875500BT Fetal Bovine Serum Bioexplorer Cat# BS1612-109 Penicillin-Streptomycin solution Biosharp Cat# BL505A Sodium lactate MedChemExpress Cat# HY-B2227B Oxamate MedChem Express Cat# HY-W013032A CCK-8 solution APExBIO Houston Cat# K1018 Matrigel Matrix Corning Cat# 354234 FITC-Dextran (40 kDa) Beyotime Cat# ST2930 RIPA lysis buffer Sigma-Aldrich Cat# 20-188 Protease inhibitor cocktail Sigma-Aldrich Cat# P8340 anti-FLAG M2 magnetic beads Sigma Cat# A2220 Evans Blue Sigma-Aldrich Cat# E2129 Anti-FLAG M2 magnetic beads Sigma-Aldrich Cat# A2220 ECL Prime Cytiva Cat# RPN2236; RPN2232 DAPI Sigma-Aldrich Cat# S7113 Critical commercial assays Annexin V-FITC Apoptosis Detection Kit Beyotime Cat# C1062M TUNEL Kit Beyotime Cat# C1086 Lactate Assay Kit Cayman Chemical Cat# 700510 BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23227 TMT Mass Tagging Kit Thermo Fisher Scientific Cat# 90064B RNAiso Plus Takara Cat# 9109 HiScript II Q RT SuperMix for qPCR (+gDNA wiper) Vazyme Cat# R223-01 ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-02 ACQUITY UPLC Waters N/A ESI source Fisher Scientific N/A Experimental models: Cell lines bEnd.3 (mouse brain endothelial cells) American Type Culture Collection (ATCC) N/A Experimental models: Organisms/strains Mouse: C57BL/6J (6–8 weeks old) Weitong Lihua Laboratory Animal Technology Co., Ltd N/A (Continued on next page) 18 Cell Reports 45, 117317, May 26, 2026
Polymerase Chain Reaction:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Cloning:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Mutagenesis:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Concentration Assay:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Sequencing:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
RNA sequencing:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Negative Control:Article Title: Host microRNA-31-5p regulates KHDRBS3 expression and modulates viral gene expression during KSHV lytic reactivation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER RNase-Free DNase Set Qiagen Cat#79254 QIAshredder Qiagen Cat#79654 Critical commercial assays Dual-Luciferase Reporter Assay Promega Cat#E1910 LightCycler 480 SYBR Green I Master Roche Cat#04707516001 miScript II RT Kit Qiagen Cat#218160 miScript SYBR Green PCR Kit Qiagen Cat#218073 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090010 Zero Blunt TOPO PCR Cloning Kit Thermo Fisher Scientific Cat#K2800J10 QuikChange Lightening Site-Directed Mutagenesis Kit Agilent Technologies Cat#210518 mirVana miRNA Isolation Kit Thermo Fisher Scientific Cat#AM1560 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat23225 MycoAlert Mycoplasma Detection Kit Lonza Cat#LT07-318 RNA Clean-up and Concentration Kit Norgen Biotek Cat#61000 miRNeasy Mini Kit Qiagen Cat#217004 Deposited Data Small-RNA sequencing raw and analyzed data This paper GEO: GSE281295 RRID: SCR_005012 RNA-sequencing raw and analyzed data This paper GEO: GSE281293 RRID: SCR_005012 Experimental models: Cell lines iSLK cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A iSLK.219 cell line31 Laboratory of Kenneth Kaye, Harvard Medical School N/A TREx BCBL1-Rta cell line96 Laboratory of Kenneth Kaye, Harvard Medical School N/A Oligonucleotides mirVana miRNA mimic, hsa-miR-31-5p, assay ID: MC11465 Thermo Fisher Scientific Cat#4464066 mirVana miRNA mimic, Negative Control No. 1 Thermo Fisher Scientific Cat#4464059 mirVana miRNA inhibitor, hsa-miR-31-5p, assay ID: MH11465 Thermo Fisher Scientific Cat#4464084 mirVana miRNA inhibitor, Negative Control No. 1 Thermo Fisher Scientific Cat#4464076 Silencer Select siRNA KHDRBS3 #1, assay ID: s20950 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA KHDRBS3 #2, assay ID: s20949 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #1, assay ID: s225837 Thermo Fisher Scientific Cat#4392420 Silencer Select siRNA SLC51A #2, assay ID: s47293 Thermo Fisher Scientific Cat#4392420 SilencerTM Select Negative Control No. 1 siRNA Thermo Fisher Scientific Cat#4390843 Hs_GAPDH_1_SG QuantiTect Primer Assay QT00079247 Qiagen Cat#249900 Hs_CD109_1_SG QuantiTect Primer Assay QT00064589 Qiagen Cat#249900 Hs_CKAP4_1_SG QuantiTect Primer Assay QT00203245 Qiagen Cat#249900 Hs_IFIT1_1_SG QuantiTect Primer Assay QT00201012 Qiagen Cat#249900 Hs_KHDRBS3_1_SG QuantiTect Primer Assay QT00065296 Qiagen Cat#249900 Hs_NNMT_1_SG QuantiTect Primer Assay QT00076041 Qiagen Cat#249900 (Continued on next page) 18 Cell Reports 45, 117160, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Hs_SAR1A_1_SG QuantiTect Primer Assay QT00082173 Qiagen Cat#249900 Hs_SSH1_1_SG QuantiTect Primer Assay QT00011417 Qiagen Cat#249900 Hs_STOM_1_SG QuantiTect Primer Assay QT00033152 Qiagen Cat#249900 Hs_TRIM59_1_SG QuantiTect Primer Assay QT00047166 Qiagen Cat#249900 Hs_YPEL2_1_SG QuantiTect Primer Assay QT00069482 Qiagen Cat#249900 Hs_AGT_1_SG QuantiTect Primer Assay QT00005614 Qiagen Cat#249900 Hs_C15orf39_1_SG QuantiTect Primer Assay QT00200900 Qiagen Cat#249900 Hs_C1orf198_1_SG QuantiTect Primer Assay QT02322908 Qiagen Cat#249900 Hs_DTX4_1_SG QuantiTect Primer Assay QT00197484 Qiagen Cat#249900 Hs_GSTM4_1_SG QuantiTect Primer Assay QT00046662 Qiagen Cat#249900 Hs_PAQR8_1_SG QuantiTect Primer Assay QT01028104 Qiagen Cat#249900 Hs_PLEKHO2_1_SG QuantiTect Primer Assay QT00069377 Qiagen Cat#249900 Hs_PTGFR_1_SG QuantiTect Primer Assay QT00029540 Qiagen Cat#249900 Hs_SEMA5A_1_SG QuantiTect Primer Assay QT00053417 Qiagen Cat#249900 Hs_SLC51A_1_SG QuantiTect Primer Assay QT00493059 Qiagen Cat#249900 Hs_CRISPLD2_1_SG QuantiTect Primer Assay QT00072485 Qiagen Cat#249900 qPCR primers – Table S5 Mutagenic primers – Table S5 Primers for cloning 3′ UTRs of the indicated genes into psiCHECK-2 vector – Table S5 Recombinant DNA pCMV-VSV-G was a gift from Bob Weinberg97 Addgene Addgene plasmid # 8454; http://n2t.net/ addgene:8454; RRID: Addgene_8454 psPAX2 was a gift from Didier Trono Addgene Addgene plasmid # 12260; http://n2t.net/ addgene:12260; RRID: Addgene_12260 KHDRBS3 Lentiviral Vector (pLenti-III-CMVhKHDRBS3-SV40-Blasticidin) Applied Biological Materials Cat#25507061 Lenti-CMV-SV40-Blasticidin Control Vector Applied Biological Materials Cat#LV587 KHDRBS3 sgRNA CRISPR/Cas9 All-in-One Lentivirus Applied Biological Materials Cat#255071110502 Software and Algorithms TargetScanHuman (version 7.2, March 2018)45 Whitehead Institute for Biomedical Research https://www.targetscan.org/vert_71/ Fiji (version 2.0.0-rc-69/1.52i, December 2018)98 http://imagej.net/Fiji RRID: SCR_002285 Celigo Imaging System Revvity RRID: SCR_018808 GraphPad Prism (version 8.4.3 (471), June 2020) GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 (Continued on next page) Cell Reports 45, 117160, April 28, 2026 19
Real-time Polymerase Chain Reaction:Article Title: Circuit and molecular mechanisms underlying incubation of methamphetamine craving in the prelimbic cortex.
Article Snippet: Article Circuit and molecular mechanisms underlying incubation of methamphetamine craving in the prelimbic cortex Highlights • SST and PV interneurons in the PL differentially regulate methamphetamine craving • LHGABA → PLSST and AMGlu → PLPV circuits drive stagespecific craving • KCNC2 upregulation in interneurons underlies distinct neuronal excitability changes • Specific knockdown of KCNC2 reduces craving during early and prolonged withdrawal Authors Sai Shi, Yi-Wen Sun, Jin-Jun Ding, ..., Fang Liu, Ti-Fei Yuan, Min Zhao Correspondence fang.liu@camh.ca (F.L.), ytf0707@126.com (T..-F.Y.), drminzhao@smhc.org.cn (M.Z.). In brief Shi et al. reveal that two distinct interneurons in the PL control the incubation of methamphetamine craving during different withdrawal stages.. They uncover a circuit-switch principle and propose a key molecular mediator, offering phase-specific therapeutic strategies to reduce relapse.
Multiplex Assay:Article Title: Circuit and molecular mechanisms underlying incubation of methamphetamine craving in the prelimbic cortex.
Article Snippet: Article Circuit and molecular mechanisms underlying incubation of methamphetamine craving in the prelimbic cortex Highlights • SST and PV interneurons in the PL differentially regulate methamphetamine craving • LHGABA → PLSST and AMGlu → PLPV circuits drive stagespecific craving • KCNC2 upregulation in interneurons underlies distinct neuronal excitability changes • Specific knockdown of KCNC2 reduces craving during early and prolonged withdrawal Authors Sai Shi, Yi-Wen Sun, Jin-Jun Ding, ..., Fang Liu, Ti-Fei Yuan, Min Zhao Correspondence fang.liu@camh.ca (F.L.), ytf0707@126.com (T..-F.Y.), drminzhao@smhc.org.cn (M.Z.). In brief Shi et al. reveal that two distinct interneurons in the PL control the incubation of methamphetamine craving during different withdrawal stages.. They uncover a circuit-switch principle and propose a key molecular mediator, offering phase-specific therapeutic strategies to reduce relapse.
Protease Inhibitor:Article Title: Circuit and molecular mechanisms underlying incubation of methamphetamine craving in the prelimbic cortex.
Article Snippet: Article Circuit and molecular mechanisms underlying incubation of methamphetamine craving in the prelimbic cortex Highlights • SST and PV interneurons in the PL differentially regulate methamphetamine craving • LHGABA → PLSST and AMGlu → PLPV circuits drive stagespecific craving • KCNC2 upregulation in interneurons underlies distinct neuronal excitability changes • Specific knockdown of KCNC2 reduces craving during early and prolonged withdrawal Authors Sai Shi, Yi-Wen Sun, Jin-Jun Ding, ..., Fang Liu, Ti-Fei Yuan, Min Zhao Correspondence fang.liu@camh.ca (F.L.), ytf0707@126.com (T..-F.Y.), drminzhao@smhc.org.cn (M.Z.). In brief Shi et al. reveal that two distinct interneurons in the PL control the incubation of methamphetamine craving during different withdrawal stages.. They uncover a circuit-switch principle and propose a key molecular mediator, offering phase-specific therapeutic strategies to reduce relapse.
Lysis:Article Title: Circuit and molecular mechanisms underlying incubation of methamphetamine craving in the prelimbic cortex.
Article Snippet: Article Circuit and molecular mechanisms underlying incubation of methamphetamine craving in the prelimbic cortex Highlights • SST and PV interneurons in the PL differentially regulate methamphetamine craving • LHGABA → PLSST and AMGlu → PLPV circuits drive stagespecific craving • KCNC2 upregulation in interneurons underlies distinct neuronal excitability changes • Specific knockdown of KCNC2 reduces craving during early and prolonged withdrawal Authors Sai Shi, Yi-Wen Sun, Jin-Jun Ding, ..., Fang Liu, Ti-Fei Yuan, Min Zhao Correspondence fang.liu@camh.ca (F.L.), ytf0707@126.com (T..-F.Y.), drminzhao@smhc.org.cn (M.Z.). In brief Shi et al. reveal that two distinct interneurons in the PL control the incubation of methamphetamine craving during different withdrawal stages.. They uncover a circuit-switch principle and propose a key molecular mediator, offering phase-specific therapeutic strategies to reduce relapse.
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