Review



resource source identifier image j fiji nih  (Bio-Rad)


Bioz Verified Symbol Bio-Rad is a verified supplier  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
    • 99
      Buy from Supplier

    Structured Review

    Bio-Rad resource source identifier image j fiji nih
    Resource Source Identifier Image J Fiji Nih, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 99/100, based on 36323 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/source+software+fiji/Image+Lab+Software/pm41330383-1014-2-15
    Average 99 stars, based on 36323 article reviews
    resource source identifier image j fiji nih - by Bioz Stars, 2026-09
    99/100 stars

    Images

    Related Articles

    Software:

    Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll ..

    Article Title: Cross-species interactome analysis uncovers a conserved selective autophagy mechanism for protein quality control in plants.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Image J (Fiji) NIH https://imagej.nih.gov/ij/ RRID: SCR_002285 Image Lab Software BioRad http://www.bio-rad.com/en-us/sku/ 1709690-image-lab-software; RRID: SCR_014210 iBright analysis software Invitrogen RRID: SCR_017632 Adobe Illustrator 2022 Adobe Inc. https://www.adobe.com; RRID: SCR_010279 Adobe Photoshop 2023 Adobe Inc. https://www.adobe.com; RRID: SCR_014199 GraphPad Prism v9.0 GraphPad Software https://www.graphpad.com; RRID: SCR_002798 RStudio 2021.09.2+382 ‘‘Ghost Orchid’’ Release; R version 4.3.0 RStudio; The R Foundation for Statistical Computing https://www.r-project.org/ UCSF ChimeraX Resource for Biocomputing, Visualization, and Informatics (RBVI) https://www.cgl.ucsf.edu/chimerax/; RRID: SCR_015872 COOT MRC Laboratory of Molecular Biology https://www2.mrc-lmb.cam.ac.uk/ personal/pemsley/coot/; RRID: SCR_014222 PHASER v1.2 Cambridge University https://www-structmed.cimr.cam.ac.uk/ phaser_obsolete/documentation/phaser-1. .. 2.html; RRID: SCR_014219 PHENIX v1.2 The Phenix Industrial Consortium https://phenix-online.org/documentation/ index.html; RRID:SCR_014224 Other HPM100 high-pressure freezer Leica Microsystems, Austria N/A AFS2 machine Leica Microsystems, Austria N/A Hitachi H-7650 electron microscope Hitachi High-Tech Group N/A Vibrating Mill MM 400 Retsch N/A Minichiller Bioruptor® UCD-200 Diagenode Cat#B01020001 Silamat S6 Ivoclar vivadent N/A LightCycler® 96 Instrument Roche Cat#05815916001 Percival CU-36L4 Percival Scientific, inc. N/A Synergy HTX Multi-Mode Microplate Reader BioTek N/A Trans-Blot® TurboTM Transfer System BioRad Cat#1704150 ChemiDoc Touch Imaging System BioRad N/A iBright Imaging System Invitrogen N/A ll OPEN ACCESSResource Developmental Cell 61, 1–21.e1–e22, March 11, 2026 e8 All M. polymorpha lines used in this study originate from Takaragaike-1 (Tak-1) and are listed in the key resources table in STAR Methods.

    Article Title: Chimeric antigen receptor-induced antigen loss protects CD5.CART cells from fratricide without compromising on-target cytotoxicity
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Mouse anti-human TCRgd-1 PE (clone 11F2) BD Biosciences Cat#340887; RRID: AB_400172 Zombie NIR Dye Biolegend Cat#77184 TotalSeq-C0045 Mouse anti-human CD4 (clone SK3) Biolegend Cat#344651; RRID: AB_2800921 TotalSeq-C0138 Mouse anti-human CD5 (clone UCHT2) Biolegend Cat#300637; RRID: AB_2800726 TotalSeq-C0066 Mouse anti-human CD7 (CD7-6B7) Biolegend Cat#343127; RRID: AB_2800914 TotalSeq-C0046 Mouse anti-human CD8 (clone SK1) Biolegend Cat#344753; RRID: AB_2800922 TotalSeq-C0063 Mouse anti-human CD45RA (clone HI100) Biolegend Cat#304163; RRID: AB_2800764 TotalSeq-C0087 Mouse anti-human CD45RO (clone UCHL1) Biolegend Cat#304259; RRID: AB_2800766 TotalSeq-C0147 Mouse anti-human CD62L (clone DREG-56) Biolegend Cat#304851; RRID: AB_2800770 TotalSeq-C0251 Mouse anti-human Hashtag 1 (clone LNH-94; 2M2) Biolegend Cat#394661; RRID: AB_2801031 TotalSeq-C0252 Mouse anti-human Hashtag 2 (clone LNH-94; 2M2) Biolegend Cat#394663; RRID: AB_2801032 TotalSeq-C0253 Mouse anti-human Hashtag 3 (clone LNH-94; 2M2) Biolegend Cat#394665; RRID: AB_2801033 Critical commercial assays RNeasy Plus Micro Kit Qiagen Cat#74034 SuperScript III First-Strand Synthesis SuperMix Invitrogen Cat#18080-400 HiScribe T7 New England Biosciences Cat#E2040S Human soluble CD5 ELISA Kit OriGene Cat#EA100720 CD3 Microbeads, human Miltenyi Biotec Cat#130-050-101 Chromium Next GEM Single Cell 50 Kit v2 10x Genomics Cat#1000263 50 Feature Barcode Kit 10x Genomics Cat#100256 Chromium Next GEM Chip K Single Cell Kit 10x Genomics Cat#1000286 Dual Index Kit TT Set A 10x Genomics Cat#1000215 Dual Index Kit TN Set A 10x Genomics Cat#1000250 Alexa Fluor 647 Antibody Labeling Kit Thermofisher Scientific Cat#A20186 Meta Mark TCR Vb Repertoire Kit Beckman Coulter Cat#IM3497 Deposited data Western Blot Data This Paper Figures 1C, 1J, 2F, S1D; Mendeley Data: https://doi.org/10.17632/ g7g56953xg.1 Single Cell RNA-Sequencing/CITE-Sequencing Data This Paper Sequence Read Archive: SRR28525016, SRR28525017, SRR28525018, SRR28525019 Single Cell RNA-Sequencing/CITE-Sequencing Code This Paper Zenodo: https://zenodo.org/records/ 11286440 Experimental models: Cell lines CCRF-CEM ATCC Cat#CCL-119 HuT 78 ATCC Cat#TIB-161 Jurkat (clone E6-1) ATCC Cat#TIB-152 MOLT-4 ATCC Cat#CRL-1582 SUP-T1 ATCC Cat#CRL-1942 Experimental models: Organisms/strains NOD.Cg-Prkdcscid Il2rgtm1/Wjl/SzJ mice (NSG) Jackson Laboratories Strain #005557 (Continued on next page) Cell Reports Medicine 5, 101628, July 16, 2024 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides CRISPR Cas9 sgRNA targeting sequence: CD5 ttaatacgactcactataGGCGTGGTGGAGTTCTAC AGgttttagagctagaaatagc In-house N/A Software and algorithms LASAF software v3.3 Leica Microsystems https://www.leica-microsystems. com/products/microscope-software/ p/leica-las-x-ls/ ImageJ2 v2.3.0/1.53f Open source https://imagej.net/software/fiji/ downloads Image Studio v5.5.4 LI-COR Biosciences https://www.licor.com/bio/image- studio/ CFX Manager Software v3.1 Bio-Rad https://www.bio-rad.com/en-us/ product/previous-qpcr-softwarereleases?ID=OO2BB34VY BD FACS Diva v8.0 BD Biosciences N/A FlowJo v10.9.0 BD Biosciences https://www.flowjo.com/solutions/ flowjo/downloads SpectroFlo v3.2.1 Cytek Biosciences N/A GraphPad Prism v10.0.0 GraphPad https://www.graphpad.com/ how-to-buy/ Other GeneJuice EMD Milipore Cat#70967 CloneAmp HiFi PCR Premix Takara Cat#639298 LabTek II Chambered Coverglass Thermofisher Scientific Cat#155409PK Open Air Rocker Fisher Scientific Cat#88-861-025 TaqMan CD5 Probe (Hs00204397_m1) Applied Biosystems Cat#4331182 CountBright Absolute Counting Beads Thermofisher Scientific Cat#1-2222-42 TaqMan 18S Probe (Hs99999901_s1) Applied Biosystems Cat#4331182 TaqMan ACTB Probe (Hs01060665_g1 Applied Biosystems Cat#4331182 TaqMan B2M Probe (Hs00187842_m1) Applied Biosystems Cat#4331182 TaqMan Fast Advanced Master Mix for qPCR Applied Biosystems Cat#4444554 Article ll OPEN ACCESS ..

    Article Title: Dynamics of Free and Chromatin-Bound Histone H3 during Early Embryogenesis.
    Article Snippet: .. H3.3A-Dendra2: yw; H3.3A-Dendra2/CyO This paper N/A D. melanogaster. nos-PBac Shvartsman Lab N/A D. melanogaster: His-RFP: w; His2Av-mRFP1 Bloomington Drosophila Stock Center BDSC_23651 Oligonucleotides Oligonucleotides for pMBAC-1xHisC-H3-Dendra2, pU6-H3.3A-chiRNA, and pScarlessHD-Dendra2-DsRed, see Table S2 This paper N/A Recombinant DNA pMBAC-1xHisC Duronio lab N/A Dendra2-H3.3-N-14 Davidson lab Addgene Plasmid #57725 pMBAC-1xHisC-H3-Dendra2 This paper N/A pU6-BbsI-chiRNA Harrison Lab, O’Connor-Giles Lab, Wildonger Lab Addgene Plasmid #45946 pScarlessHD-sfGFP-DsRed O’Connor-Giles Lab Addgene plasmid #80811 pU6-H3.3A-gRNA This paper N/A pScarlessHD-H3.3A-Dendra2-DsRed This paper N/A Software and Algorithms Fiji Open source https://fiji.sc/ Image Lab Bio-Rad http://www.bio-rad.com/en-us/product/ image-lab-software?ID=KRE6P5E8Z ..

    Article Title: The phosphodiesterase 2A controls lymphatic junctional maturation via cGMP-dependent notch signaling.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines HDLECs PromoCell Cat# C-12216 HUVECs PromoCell Cat# C-12203 mECs This manuscript N/A Experimental models: Organisms/strains Mouse: Tie2-Cre (B6.Cg-Tg(Tek-cre) 1Ywa/J) Kisanuki et al.69 RRID:IMSR_JAX:008863 Mouse: Cdh5-CreERT2 (Tg(Cdh5-cre/ ERT2)1Rha) Sörensen et al.70 RRID:IMSR_EM:14891 Mouse: Prox1-CreERT2 (Tg(Prox1-cre/ ERT2)1Tmak Bazigou et al.71 RRID:IMSR_EM:13737 Mouse: Pde2a global knockout (B6; 129P2487Pde2A < tm1Dgen>/H; EM: 02366) Assenza et al.25 RRID:IMSR_EM:02366 Mouse: Pde2a (Pde2atm1a(EUCOMM)Wtsl) This manuscript N/A Oligonucleotides AllStars Negative CTRL siRNA Qiagen Cat# 1027281 FlexiTube PDE2A siRNA Qiagen Cat# SI00040159 DLL1 (hs00194509_m1) Thermo Fischer Scientific Cat# 4331182 GAPDH (hs99999905) Thermo Fischer Scientific Cat# 4326317E Gapdh (mm99999915_g1) Thermo Fischer Scientific Cat# 4352932E GJA4 (hs00704917_s1) Thermo Fischer Scientific Cat# 4331182 Hey1 (mm00468865_m1) Thermo Fischer Scientific Cat# 4331182 miR-139-5p (MI0000693) Thermo Fischer Scientific Cat# 002289 Mki67 (mm01278617_m1) Thermo Fischer Scientific Cat# 4331182 PDE10A (hs01098928_m1) Thermo Fischer Scientific Cat# 4351372 PDE12 (hs00698272_m1) Thermo Fischer Scientific Cat# 4331182 PDE2A (hs00159935_m1) Thermo Fischer Scientific Cat# 4331182 Pde2a (mm01136644_m1) Thermo Fischer Scientific Cat# 4331182 PDE3A (hs01012698_m1) Thermo Fischer Scientific Cat# 4331182 PDE4B (hs00963643_m1) Thermo Fischer Scientific Cat# 4331182 PDE4D (hs01579625_m1) Thermo Fischer Scientific Cat# 4331182 PDE6D (hs01062025_m1) Thermo Fischer Scientific Cat# 4331182 PDE8A (hs01079617_m1) Thermo Fischer Scientific Cat# 4331182 PSEN2 (hs01577197_m1) Thermo Fischer Scientific Cat# 4331182 RNU48 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001006 snoRNA202 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001232 snoRNA234 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001234 Pde2a-5’-arm 50ACTGGTCAGTTCTGAGC CTCACCC 30 This paper N/A Pde2a-3’-arm 50 AGTCTGGACTCCCCA TCTAGCAGG 30 This paper N/A Cre transgene sense 50GAACCTGATGG ACATGTTCAGG 30 This paper N/A Cre transgene antisense 50 AGTGCGTT CGAACGCTAGAGCCTGT 30 This paper N/A Myogenin sense 50 TTACGTCCA TCGTGGACAGC 30 This paper N/A Myogenin antisense 50 TGGGCTGGGT GTTAGCCTTA 30 This paper N/A (Continued on next page) e4 Developmental Cell 59, 1–18.e1–e11, February 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms BioRad Image Lab Software BioRad N/A Diva 8.0.1 software BD Biosciences N/A Fiji ImageJ N/A https://imagej.net/ij/ GraphPad Prism 9 Dotmatics N/A Leica LAS-X software Leica N/A MicroManager 1.4 software Open source N/A Seurat package Satija et al.72 https://www.nature.com/articles/nbt.3192 umap package McInnes et al.73 https://joss.theoj.org/papers/10.21105/ joss.00861 Plotly software Open source https://plotly.com/r/ FastQC (v0.11.9) Open source http://www.bioinformatics.babraham.ac. uk/projects/fastqc/ Trimmomatic (v0.36) Bolger et al.74 https://academic.oup.com/bioinformatics/ article/30/15/2114/2390096?login=true STAR (v2.7.3a) Dobin et al.75 https://academic.oup.com/bioinformatics/ article/29/1/15/272537 ComBat-seq Zhang et al.76 https://academic.oup.com/nargab/article/ 2/3/lqaa078/5909519?searchresult=1 WebGestalt platform 2019 Liao et al.77 https://academic.oup.com/nar/article/47/ W1/W199/5494758?login=true Other 24-well Plate Softwell Easy Coat hydrogels (0.1, 1, 2, 4 and 25kPa) Matrigen Cat# SS24-EC 8-well Lab-Tek II chamber slides Lab-Tek Cat# 154941 Agilent Technologies 2100 bioanalyzer Agilent https://www.agilent.com/en/product/ automated-electrophoresis/bioanalyzersystems/bioanalyzer-instrument AMPure XP magnetic beads Beckman Cat# A53880 Axiocam 208 Color Zeiss N/A BD Biosciences FACSAria IIIu BD Biosciences N/A CoolLED beam-splitter DV2 Dual View Photometrics N/A CMOS camera chip OptiMOS, Qimaging N/A DEAE-Sephadex A-25 columns Cytiva Cat# 17017001 DynaMag -2 Invitrogen Cat# 12321D Gel Doc MP Imaging System BioRad N/A Hamilton TLC syringe Sigma-Aldrich Cat# HAM7635-01-1EA Immobilion -P Transfer Membrane (0.45mm pore size) Merck Cat# IPVH00010 Inject -F syringe Braun Cat# 9166017V Leica DMI 3000 B inverted fluorescent microscope Leica N/A Leica SP8 inverted microscope Leica N/A Nikon Eclipse Ts2R microscope Nikon N/A Sheep-anti-rat IgG Dynabeads Invitrogen Cat# 110-35 StepOnePlus RT PCR system Applied Biosystems N/A Tecan Spark 10M microplate reader Tecan N/A Tissue culture-treated dishes Corning Cat# 430167 Tissue culture-treated dishes (60mm) Corning Cat# 430166 Transwell filters (0.4mm pore size) Corning Cat# 3413 (Continued on next page) Developmental Cell 59, 1–18.e1–e11, February 5, 2024 e5 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tri-Carb 2100TR Liquid Scintillation Counter Packard Instruments Cat# 2000CA ULTIMA GOLD scintillation liquid PerkinElmer Cat# 6013326 UltraComp eBeads Plus Compensation Beads Invitrogen Cat# 01-3333-42 Zeiss Stemi 508 Zeiss N/A

    Clinical Proteomics:

    Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll ..

    Transfection:

    Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll ..

    Blocking Assay:

    Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll ..

    SYBR Green Assay:

    Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll ..

    Polymerase Chain Reaction:

    Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll ..

    Article Title: Chimeric antigen receptor-induced antigen loss protects CD5.CART cells from fratricide without compromising on-target cytotoxicity
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Mouse anti-human TCRgd-1 PE (clone 11F2) BD Biosciences Cat#340887; RRID: AB_400172 Zombie NIR Dye Biolegend Cat#77184 TotalSeq-C0045 Mouse anti-human CD4 (clone SK3) Biolegend Cat#344651; RRID: AB_2800921 TotalSeq-C0138 Mouse anti-human CD5 (clone UCHT2) Biolegend Cat#300637; RRID: AB_2800726 TotalSeq-C0066 Mouse anti-human CD7 (CD7-6B7) Biolegend Cat#343127; RRID: AB_2800914 TotalSeq-C0046 Mouse anti-human CD8 (clone SK1) Biolegend Cat#344753; RRID: AB_2800922 TotalSeq-C0063 Mouse anti-human CD45RA (clone HI100) Biolegend Cat#304163; RRID: AB_2800764 TotalSeq-C0087 Mouse anti-human CD45RO (clone UCHL1) Biolegend Cat#304259; RRID: AB_2800766 TotalSeq-C0147 Mouse anti-human CD62L (clone DREG-56) Biolegend Cat#304851; RRID: AB_2800770 TotalSeq-C0251 Mouse anti-human Hashtag 1 (clone LNH-94; 2M2) Biolegend Cat#394661; RRID: AB_2801031 TotalSeq-C0252 Mouse anti-human Hashtag 2 (clone LNH-94; 2M2) Biolegend Cat#394663; RRID: AB_2801032 TotalSeq-C0253 Mouse anti-human Hashtag 3 (clone LNH-94; 2M2) Biolegend Cat#394665; RRID: AB_2801033 Critical commercial assays RNeasy Plus Micro Kit Qiagen Cat#74034 SuperScript III First-Strand Synthesis SuperMix Invitrogen Cat#18080-400 HiScribe T7 New England Biosciences Cat#E2040S Human soluble CD5 ELISA Kit OriGene Cat#EA100720 CD3 Microbeads, human Miltenyi Biotec Cat#130-050-101 Chromium Next GEM Single Cell 50 Kit v2 10x Genomics Cat#1000263 50 Feature Barcode Kit 10x Genomics Cat#100256 Chromium Next GEM Chip K Single Cell Kit 10x Genomics Cat#1000286 Dual Index Kit TT Set A 10x Genomics Cat#1000215 Dual Index Kit TN Set A 10x Genomics Cat#1000250 Alexa Fluor 647 Antibody Labeling Kit Thermofisher Scientific Cat#A20186 Meta Mark TCR Vb Repertoire Kit Beckman Coulter Cat#IM3497 Deposited data Western Blot Data This Paper Figures 1C, 1J, 2F, S1D; Mendeley Data: https://doi.org/10.17632/ g7g56953xg.1 Single Cell RNA-Sequencing/CITE-Sequencing Data This Paper Sequence Read Archive: SRR28525016, SRR28525017, SRR28525018, SRR28525019 Single Cell RNA-Sequencing/CITE-Sequencing Code This Paper Zenodo: https://zenodo.org/records/ 11286440 Experimental models: Cell lines CCRF-CEM ATCC Cat#CCL-119 HuT 78 ATCC Cat#TIB-161 Jurkat (clone E6-1) ATCC Cat#TIB-152 MOLT-4 ATCC Cat#CRL-1582 SUP-T1 ATCC Cat#CRL-1942 Experimental models: Organisms/strains NOD.Cg-Prkdcscid Il2rgtm1/Wjl/SzJ mice (NSG) Jackson Laboratories Strain #005557 (Continued on next page) Cell Reports Medicine 5, 101628, July 16, 2024 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides CRISPR Cas9 sgRNA targeting sequence: CD5 ttaatacgactcactataGGCGTGGTGGAGTTCTAC AGgttttagagctagaaatagc In-house N/A Software and algorithms LASAF software v3.3 Leica Microsystems https://www.leica-microsystems. com/products/microscope-software/ p/leica-las-x-ls/ ImageJ2 v2.3.0/1.53f Open source https://imagej.net/software/fiji/ downloads Image Studio v5.5.4 LI-COR Biosciences https://www.licor.com/bio/image- studio/ CFX Manager Software v3.1 Bio-Rad https://www.bio-rad.com/en-us/ product/previous-qpcr-softwarereleases?ID=OO2BB34VY BD FACS Diva v8.0 BD Biosciences N/A FlowJo v10.9.0 BD Biosciences https://www.flowjo.com/solutions/ flowjo/downloads SpectroFlo v3.2.1 Cytek Biosciences N/A GraphPad Prism v10.0.0 GraphPad https://www.graphpad.com/ how-to-buy/ Other GeneJuice EMD Milipore Cat#70967 CloneAmp HiFi PCR Premix Takara Cat#639298 LabTek II Chambered Coverglass Thermofisher Scientific Cat#155409PK Open Air Rocker Fisher Scientific Cat#88-861-025 TaqMan CD5 Probe (Hs00204397_m1) Applied Biosystems Cat#4331182 CountBright Absolute Counting Beads Thermofisher Scientific Cat#1-2222-42 TaqMan 18S Probe (Hs99999901_s1) Applied Biosystems Cat#4331182 TaqMan ACTB Probe (Hs01060665_g1 Applied Biosystems Cat#4331182 TaqMan B2M Probe (Hs00187842_m1) Applied Biosystems Cat#4331182 TaqMan Fast Advanced Master Mix for qPCR Applied Biosystems Cat#4444554 Article ll OPEN ACCESS ..

    Lysis:

    Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll ..

    Extraction:

    Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll ..

    Marker:

    Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll ..

    Adhesive:

    Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll ..

    Western Blot:

    Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll ..

    CRISPR:

    Article Title: Chimeric antigen receptor-induced antigen loss protects CD5.CART cells from fratricide without compromising on-target cytotoxicity
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Mouse anti-human TCRgd-1 PE (clone 11F2) BD Biosciences Cat#340887; RRID: AB_400172 Zombie NIR Dye Biolegend Cat#77184 TotalSeq-C0045 Mouse anti-human CD4 (clone SK3) Biolegend Cat#344651; RRID: AB_2800921 TotalSeq-C0138 Mouse anti-human CD5 (clone UCHT2) Biolegend Cat#300637; RRID: AB_2800726 TotalSeq-C0066 Mouse anti-human CD7 (CD7-6B7) Biolegend Cat#343127; RRID: AB_2800914 TotalSeq-C0046 Mouse anti-human CD8 (clone SK1) Biolegend Cat#344753; RRID: AB_2800922 TotalSeq-C0063 Mouse anti-human CD45RA (clone HI100) Biolegend Cat#304163; RRID: AB_2800764 TotalSeq-C0087 Mouse anti-human CD45RO (clone UCHL1) Biolegend Cat#304259; RRID: AB_2800766 TotalSeq-C0147 Mouse anti-human CD62L (clone DREG-56) Biolegend Cat#304851; RRID: AB_2800770 TotalSeq-C0251 Mouse anti-human Hashtag 1 (clone LNH-94; 2M2) Biolegend Cat#394661; RRID: AB_2801031 TotalSeq-C0252 Mouse anti-human Hashtag 2 (clone LNH-94; 2M2) Biolegend Cat#394663; RRID: AB_2801032 TotalSeq-C0253 Mouse anti-human Hashtag 3 (clone LNH-94; 2M2) Biolegend Cat#394665; RRID: AB_2801033 Critical commercial assays RNeasy Plus Micro Kit Qiagen Cat#74034 SuperScript III First-Strand Synthesis SuperMix Invitrogen Cat#18080-400 HiScribe T7 New England Biosciences Cat#E2040S Human soluble CD5 ELISA Kit OriGene Cat#EA100720 CD3 Microbeads, human Miltenyi Biotec Cat#130-050-101 Chromium Next GEM Single Cell 50 Kit v2 10x Genomics Cat#1000263 50 Feature Barcode Kit 10x Genomics Cat#100256 Chromium Next GEM Chip K Single Cell Kit 10x Genomics Cat#1000286 Dual Index Kit TT Set A 10x Genomics Cat#1000215 Dual Index Kit TN Set A 10x Genomics Cat#1000250 Alexa Fluor 647 Antibody Labeling Kit Thermofisher Scientific Cat#A20186 Meta Mark TCR Vb Repertoire Kit Beckman Coulter Cat#IM3497 Deposited data Western Blot Data This Paper Figures 1C, 1J, 2F, S1D; Mendeley Data: https://doi.org/10.17632/ g7g56953xg.1 Single Cell RNA-Sequencing/CITE-Sequencing Data This Paper Sequence Read Archive: SRR28525016, SRR28525017, SRR28525018, SRR28525019 Single Cell RNA-Sequencing/CITE-Sequencing Code This Paper Zenodo: https://zenodo.org/records/ 11286440 Experimental models: Cell lines CCRF-CEM ATCC Cat#CCL-119 HuT 78 ATCC Cat#TIB-161 Jurkat (clone E6-1) ATCC Cat#TIB-152 MOLT-4 ATCC Cat#CRL-1582 SUP-T1 ATCC Cat#CRL-1942 Experimental models: Organisms/strains NOD.Cg-Prkdcscid Il2rgtm1/Wjl/SzJ mice (NSG) Jackson Laboratories Strain #005557 (Continued on next page) Cell Reports Medicine 5, 101628, July 16, 2024 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides CRISPR Cas9 sgRNA targeting sequence: CD5 ttaatacgactcactataGGCGTGGTGGAGTTCTAC AGgttttagagctagaaatagc In-house N/A Software and algorithms LASAF software v3.3 Leica Microsystems https://www.leica-microsystems. com/products/microscope-software/ p/leica-las-x-ls/ ImageJ2 v2.3.0/1.53f Open source https://imagej.net/software/fiji/ downloads Image Studio v5.5.4 LI-COR Biosciences https://www.licor.com/bio/image- studio/ CFX Manager Software v3.1 Bio-Rad https://www.bio-rad.com/en-us/ product/previous-qpcr-softwarereleases?ID=OO2BB34VY BD FACS Diva v8.0 BD Biosciences N/A FlowJo v10.9.0 BD Biosciences https://www.flowjo.com/solutions/ flowjo/downloads SpectroFlo v3.2.1 Cytek Biosciences N/A GraphPad Prism v10.0.0 GraphPad https://www.graphpad.com/ how-to-buy/ Other GeneJuice EMD Milipore Cat#70967 CloneAmp HiFi PCR Premix Takara Cat#639298 LabTek II Chambered Coverglass Thermofisher Scientific Cat#155409PK Open Air Rocker Fisher Scientific Cat#88-861-025 TaqMan CD5 Probe (Hs00204397_m1) Applied Biosystems Cat#4331182 CountBright Absolute Counting Beads Thermofisher Scientific Cat#1-2222-42 TaqMan 18S Probe (Hs99999901_s1) Applied Biosystems Cat#4331182 TaqMan ACTB Probe (Hs01060665_g1 Applied Biosystems Cat#4331182 TaqMan B2M Probe (Hs00187842_m1) Applied Biosystems Cat#4331182 TaqMan Fast Advanced Master Mix for qPCR Applied Biosystems Cat#4444554 Article ll OPEN ACCESS ..

    Sequencing:

    Article Title: Chimeric antigen receptor-induced antigen loss protects CD5.CART cells from fratricide without compromising on-target cytotoxicity
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Mouse anti-human TCRgd-1 PE (clone 11F2) BD Biosciences Cat#340887; RRID: AB_400172 Zombie NIR Dye Biolegend Cat#77184 TotalSeq-C0045 Mouse anti-human CD4 (clone SK3) Biolegend Cat#344651; RRID: AB_2800921 TotalSeq-C0138 Mouse anti-human CD5 (clone UCHT2) Biolegend Cat#300637; RRID: AB_2800726 TotalSeq-C0066 Mouse anti-human CD7 (CD7-6B7) Biolegend Cat#343127; RRID: AB_2800914 TotalSeq-C0046 Mouse anti-human CD8 (clone SK1) Biolegend Cat#344753; RRID: AB_2800922 TotalSeq-C0063 Mouse anti-human CD45RA (clone HI100) Biolegend Cat#304163; RRID: AB_2800764 TotalSeq-C0087 Mouse anti-human CD45RO (clone UCHL1) Biolegend Cat#304259; RRID: AB_2800766 TotalSeq-C0147 Mouse anti-human CD62L (clone DREG-56) Biolegend Cat#304851; RRID: AB_2800770 TotalSeq-C0251 Mouse anti-human Hashtag 1 (clone LNH-94; 2M2) Biolegend Cat#394661; RRID: AB_2801031 TotalSeq-C0252 Mouse anti-human Hashtag 2 (clone LNH-94; 2M2) Biolegend Cat#394663; RRID: AB_2801032 TotalSeq-C0253 Mouse anti-human Hashtag 3 (clone LNH-94; 2M2) Biolegend Cat#394665; RRID: AB_2801033 Critical commercial assays RNeasy Plus Micro Kit Qiagen Cat#74034 SuperScript III First-Strand Synthesis SuperMix Invitrogen Cat#18080-400 HiScribe T7 New England Biosciences Cat#E2040S Human soluble CD5 ELISA Kit OriGene Cat#EA100720 CD3 Microbeads, human Miltenyi Biotec Cat#130-050-101 Chromium Next GEM Single Cell 50 Kit v2 10x Genomics Cat#1000263 50 Feature Barcode Kit 10x Genomics Cat#100256 Chromium Next GEM Chip K Single Cell Kit 10x Genomics Cat#1000286 Dual Index Kit TT Set A 10x Genomics Cat#1000215 Dual Index Kit TN Set A 10x Genomics Cat#1000250 Alexa Fluor 647 Antibody Labeling Kit Thermofisher Scientific Cat#A20186 Meta Mark TCR Vb Repertoire Kit Beckman Coulter Cat#IM3497 Deposited data Western Blot Data This Paper Figures 1C, 1J, 2F, S1D; Mendeley Data: https://doi.org/10.17632/ g7g56953xg.1 Single Cell RNA-Sequencing/CITE-Sequencing Data This Paper Sequence Read Archive: SRR28525016, SRR28525017, SRR28525018, SRR28525019 Single Cell RNA-Sequencing/CITE-Sequencing Code This Paper Zenodo: https://zenodo.org/records/ 11286440 Experimental models: Cell lines CCRF-CEM ATCC Cat#CCL-119 HuT 78 ATCC Cat#TIB-161 Jurkat (clone E6-1) ATCC Cat#TIB-152 MOLT-4 ATCC Cat#CRL-1582 SUP-T1 ATCC Cat#CRL-1942 Experimental models: Organisms/strains NOD.Cg-Prkdcscid Il2rgtm1/Wjl/SzJ mice (NSG) Jackson Laboratories Strain #005557 (Continued on next page) Cell Reports Medicine 5, 101628, July 16, 2024 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides CRISPR Cas9 sgRNA targeting sequence: CD5 ttaatacgactcactataGGCGTGGTGGAGTTCTAC AGgttttagagctagaaatagc In-house N/A Software and algorithms LASAF software v3.3 Leica Microsystems https://www.leica-microsystems. com/products/microscope-software/ p/leica-las-x-ls/ ImageJ2 v2.3.0/1.53f Open source https://imagej.net/software/fiji/ downloads Image Studio v5.5.4 LI-COR Biosciences https://www.licor.com/bio/image- studio/ CFX Manager Software v3.1 Bio-Rad https://www.bio-rad.com/en-us/ product/previous-qpcr-softwarereleases?ID=OO2BB34VY BD FACS Diva v8.0 BD Biosciences N/A FlowJo v10.9.0 BD Biosciences https://www.flowjo.com/solutions/ flowjo/downloads SpectroFlo v3.2.1 Cytek Biosciences N/A GraphPad Prism v10.0.0 GraphPad https://www.graphpad.com/ how-to-buy/ Other GeneJuice EMD Milipore Cat#70967 CloneAmp HiFi PCR Premix Takara Cat#639298 LabTek II Chambered Coverglass Thermofisher Scientific Cat#155409PK Open Air Rocker Fisher Scientific Cat#88-861-025 TaqMan CD5 Probe (Hs00204397_m1) Applied Biosystems Cat#4331182 CountBright Absolute Counting Beads Thermofisher Scientific Cat#1-2222-42 TaqMan 18S Probe (Hs99999901_s1) Applied Biosystems Cat#4331182 TaqMan ACTB Probe (Hs01060665_g1 Applied Biosystems Cat#4331182 TaqMan B2M Probe (Hs00187842_m1) Applied Biosystems Cat#4331182 TaqMan Fast Advanced Master Mix for qPCR Applied Biosystems Cat#4444554 Article ll OPEN ACCESS ..

    FACS:

    Article Title: Chimeric antigen receptor-induced antigen loss protects CD5.CART cells from fratricide without compromising on-target cytotoxicity
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Mouse anti-human TCRgd-1 PE (clone 11F2) BD Biosciences Cat#340887; RRID: AB_400172 Zombie NIR Dye Biolegend Cat#77184 TotalSeq-C0045 Mouse anti-human CD4 (clone SK3) Biolegend Cat#344651; RRID: AB_2800921 TotalSeq-C0138 Mouse anti-human CD5 (clone UCHT2) Biolegend Cat#300637; RRID: AB_2800726 TotalSeq-C0066 Mouse anti-human CD7 (CD7-6B7) Biolegend Cat#343127; RRID: AB_2800914 TotalSeq-C0046 Mouse anti-human CD8 (clone SK1) Biolegend Cat#344753; RRID: AB_2800922 TotalSeq-C0063 Mouse anti-human CD45RA (clone HI100) Biolegend Cat#304163; RRID: AB_2800764 TotalSeq-C0087 Mouse anti-human CD45RO (clone UCHL1) Biolegend Cat#304259; RRID: AB_2800766 TotalSeq-C0147 Mouse anti-human CD62L (clone DREG-56) Biolegend Cat#304851; RRID: AB_2800770 TotalSeq-C0251 Mouse anti-human Hashtag 1 (clone LNH-94; 2M2) Biolegend Cat#394661; RRID: AB_2801031 TotalSeq-C0252 Mouse anti-human Hashtag 2 (clone LNH-94; 2M2) Biolegend Cat#394663; RRID: AB_2801032 TotalSeq-C0253 Mouse anti-human Hashtag 3 (clone LNH-94; 2M2) Biolegend Cat#394665; RRID: AB_2801033 Critical commercial assays RNeasy Plus Micro Kit Qiagen Cat#74034 SuperScript III First-Strand Synthesis SuperMix Invitrogen Cat#18080-400 HiScribe T7 New England Biosciences Cat#E2040S Human soluble CD5 ELISA Kit OriGene Cat#EA100720 CD3 Microbeads, human Miltenyi Biotec Cat#130-050-101 Chromium Next GEM Single Cell 50 Kit v2 10x Genomics Cat#1000263 50 Feature Barcode Kit 10x Genomics Cat#100256 Chromium Next GEM Chip K Single Cell Kit 10x Genomics Cat#1000286 Dual Index Kit TT Set A 10x Genomics Cat#1000215 Dual Index Kit TN Set A 10x Genomics Cat#1000250 Alexa Fluor 647 Antibody Labeling Kit Thermofisher Scientific Cat#A20186 Meta Mark TCR Vb Repertoire Kit Beckman Coulter Cat#IM3497 Deposited data Western Blot Data This Paper Figures 1C, 1J, 2F, S1D; Mendeley Data: https://doi.org/10.17632/ g7g56953xg.1 Single Cell RNA-Sequencing/CITE-Sequencing Data This Paper Sequence Read Archive: SRR28525016, SRR28525017, SRR28525018, SRR28525019 Single Cell RNA-Sequencing/CITE-Sequencing Code This Paper Zenodo: https://zenodo.org/records/ 11286440 Experimental models: Cell lines CCRF-CEM ATCC Cat#CCL-119 HuT 78 ATCC Cat#TIB-161 Jurkat (clone E6-1) ATCC Cat#TIB-152 MOLT-4 ATCC Cat#CRL-1582 SUP-T1 ATCC Cat#CRL-1942 Experimental models: Organisms/strains NOD.Cg-Prkdcscid Il2rgtm1/Wjl/SzJ mice (NSG) Jackson Laboratories Strain #005557 (Continued on next page) Cell Reports Medicine 5, 101628, July 16, 2024 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides CRISPR Cas9 sgRNA targeting sequence: CD5 ttaatacgactcactataGGCGTGGTGGAGTTCTAC AGgttttagagctagaaatagc In-house N/A Software and algorithms LASAF software v3.3 Leica Microsystems https://www.leica-microsystems. com/products/microscope-software/ p/leica-las-x-ls/ ImageJ2 v2.3.0/1.53f Open source https://imagej.net/software/fiji/ downloads Image Studio v5.5.4 LI-COR Biosciences https://www.licor.com/bio/image- studio/ CFX Manager Software v3.1 Bio-Rad https://www.bio-rad.com/en-us/ product/previous-qpcr-softwarereleases?ID=OO2BB34VY BD FACS Diva v8.0 BD Biosciences N/A FlowJo v10.9.0 BD Biosciences https://www.flowjo.com/solutions/ flowjo/downloads SpectroFlo v3.2.1 Cytek Biosciences N/A GraphPad Prism v10.0.0 GraphPad https://www.graphpad.com/ how-to-buy/ Other GeneJuice EMD Milipore Cat#70967 CloneAmp HiFi PCR Premix Takara Cat#639298 LabTek II Chambered Coverglass Thermofisher Scientific Cat#155409PK Open Air Rocker Fisher Scientific Cat#88-861-025 TaqMan CD5 Probe (Hs00204397_m1) Applied Biosystems Cat#4331182 CountBright Absolute Counting Beads Thermofisher Scientific Cat#1-2222-42 TaqMan 18S Probe (Hs99999901_s1) Applied Biosystems Cat#4331182 TaqMan ACTB Probe (Hs01060665_g1 Applied Biosystems Cat#4331182 TaqMan B2M Probe (Hs00187842_m1) Applied Biosystems Cat#4331182 TaqMan Fast Advanced Master Mix for qPCR Applied Biosystems Cat#4444554 Article ll OPEN ACCESS ..

    Real-time Polymerase Chain Reaction:

    Article Title: Chimeric antigen receptor-induced antigen loss protects CD5.CART cells from fratricide without compromising on-target cytotoxicity
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Mouse anti-human TCRgd-1 PE (clone 11F2) BD Biosciences Cat#340887; RRID: AB_400172 Zombie NIR Dye Biolegend Cat#77184 TotalSeq-C0045 Mouse anti-human CD4 (clone SK3) Biolegend Cat#344651; RRID: AB_2800921 TotalSeq-C0138 Mouse anti-human CD5 (clone UCHT2) Biolegend Cat#300637; RRID: AB_2800726 TotalSeq-C0066 Mouse anti-human CD7 (CD7-6B7) Biolegend Cat#343127; RRID: AB_2800914 TotalSeq-C0046 Mouse anti-human CD8 (clone SK1) Biolegend Cat#344753; RRID: AB_2800922 TotalSeq-C0063 Mouse anti-human CD45RA (clone HI100) Biolegend Cat#304163; RRID: AB_2800764 TotalSeq-C0087 Mouse anti-human CD45RO (clone UCHL1) Biolegend Cat#304259; RRID: AB_2800766 TotalSeq-C0147 Mouse anti-human CD62L (clone DREG-56) Biolegend Cat#304851; RRID: AB_2800770 TotalSeq-C0251 Mouse anti-human Hashtag 1 (clone LNH-94; 2M2) Biolegend Cat#394661; RRID: AB_2801031 TotalSeq-C0252 Mouse anti-human Hashtag 2 (clone LNH-94; 2M2) Biolegend Cat#394663; RRID: AB_2801032 TotalSeq-C0253 Mouse anti-human Hashtag 3 (clone LNH-94; 2M2) Biolegend Cat#394665; RRID: AB_2801033 Critical commercial assays RNeasy Plus Micro Kit Qiagen Cat#74034 SuperScript III First-Strand Synthesis SuperMix Invitrogen Cat#18080-400 HiScribe T7 New England Biosciences Cat#E2040S Human soluble CD5 ELISA Kit OriGene Cat#EA100720 CD3 Microbeads, human Miltenyi Biotec Cat#130-050-101 Chromium Next GEM Single Cell 50 Kit v2 10x Genomics Cat#1000263 50 Feature Barcode Kit 10x Genomics Cat#100256 Chromium Next GEM Chip K Single Cell Kit 10x Genomics Cat#1000286 Dual Index Kit TT Set A 10x Genomics Cat#1000215 Dual Index Kit TN Set A 10x Genomics Cat#1000250 Alexa Fluor 647 Antibody Labeling Kit Thermofisher Scientific Cat#A20186 Meta Mark TCR Vb Repertoire Kit Beckman Coulter Cat#IM3497 Deposited data Western Blot Data This Paper Figures 1C, 1J, 2F, S1D; Mendeley Data: https://doi.org/10.17632/ g7g56953xg.1 Single Cell RNA-Sequencing/CITE-Sequencing Data This Paper Sequence Read Archive: SRR28525016, SRR28525017, SRR28525018, SRR28525019 Single Cell RNA-Sequencing/CITE-Sequencing Code This Paper Zenodo: https://zenodo.org/records/ 11286440 Experimental models: Cell lines CCRF-CEM ATCC Cat#CCL-119 HuT 78 ATCC Cat#TIB-161 Jurkat (clone E6-1) ATCC Cat#TIB-152 MOLT-4 ATCC Cat#CRL-1582 SUP-T1 ATCC Cat#CRL-1942 Experimental models: Organisms/strains NOD.Cg-Prkdcscid Il2rgtm1/Wjl/SzJ mice (NSG) Jackson Laboratories Strain #005557 (Continued on next page) Cell Reports Medicine 5, 101628, July 16, 2024 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides CRISPR Cas9 sgRNA targeting sequence: CD5 ttaatacgactcactataGGCGTGGTGGAGTTCTAC AGgttttagagctagaaatagc In-house N/A Software and algorithms LASAF software v3.3 Leica Microsystems https://www.leica-microsystems. com/products/microscope-software/ p/leica-las-x-ls/ ImageJ2 v2.3.0/1.53f Open source https://imagej.net/software/fiji/ downloads Image Studio v5.5.4 LI-COR Biosciences https://www.licor.com/bio/image- studio/ CFX Manager Software v3.1 Bio-Rad https://www.bio-rad.com/en-us/ product/previous-qpcr-softwarereleases?ID=OO2BB34VY BD FACS Diva v8.0 BD Biosciences N/A FlowJo v10.9.0 BD Biosciences https://www.flowjo.com/solutions/ flowjo/downloads SpectroFlo v3.2.1 Cytek Biosciences N/A GraphPad Prism v10.0.0 GraphPad https://www.graphpad.com/ how-to-buy/ Other GeneJuice EMD Milipore Cat#70967 CloneAmp HiFi PCR Premix Takara Cat#639298 LabTek II Chambered Coverglass Thermofisher Scientific Cat#155409PK Open Air Rocker Fisher Scientific Cat#88-861-025 TaqMan CD5 Probe (Hs00204397_m1) Applied Biosystems Cat#4331182 CountBright Absolute Counting Beads Thermofisher Scientific Cat#1-2222-42 TaqMan 18S Probe (Hs99999901_s1) Applied Biosystems Cat#4331182 TaqMan ACTB Probe (Hs01060665_g1 Applied Biosystems Cat#4331182 TaqMan B2M Probe (Hs00187842_m1) Applied Biosystems Cat#4331182 TaqMan Fast Advanced Master Mix for qPCR Applied Biosystems Cat#4444554 Article ll OPEN ACCESS ..

    Recombinant:

    Article Title: Dynamics of Free and Chromatin-Bound Histone H3 during Early Embryogenesis.
    Article Snippet: .. H3.3A-Dendra2: yw; H3.3A-Dendra2/CyO This paper N/A D. melanogaster. nos-PBac Shvartsman Lab N/A D. melanogaster: His-RFP: w; His2Av-mRFP1 Bloomington Drosophila Stock Center BDSC_23651 Oligonucleotides Oligonucleotides for pMBAC-1xHisC-H3-Dendra2, pU6-H3.3A-chiRNA, and pScarlessHD-Dendra2-DsRed, see Table S2 This paper N/A Recombinant DNA pMBAC-1xHisC Duronio lab N/A Dendra2-H3.3-N-14 Davidson lab Addgene Plasmid #57725 pMBAC-1xHisC-H3-Dendra2 This paper N/A pU6-BbsI-chiRNA Harrison Lab, O’Connor-Giles Lab, Wildonger Lab Addgene Plasmid #45946 pScarlessHD-sfGFP-DsRed O’Connor-Giles Lab Addgene plasmid #80811 pU6-H3.3A-gRNA This paper N/A pScarlessHD-H3.3A-Dendra2-DsRed This paper N/A Software and Algorithms Fiji Open source https://fiji.sc/ Image Lab Bio-Rad http://www.bio-rad.com/en-us/product/ image-lab-software?ID=KRE6P5E8Z ..

    Plasmid Preparation:

    Article Title: Dynamics of Free and Chromatin-Bound Histone H3 during Early Embryogenesis.
    Article Snippet: .. H3.3A-Dendra2: yw; H3.3A-Dendra2/CyO This paper N/A D. melanogaster. nos-PBac Shvartsman Lab N/A D. melanogaster: His-RFP: w; His2Av-mRFP1 Bloomington Drosophila Stock Center BDSC_23651 Oligonucleotides Oligonucleotides for pMBAC-1xHisC-H3-Dendra2, pU6-H3.3A-chiRNA, and pScarlessHD-Dendra2-DsRed, see Table S2 This paper N/A Recombinant DNA pMBAC-1xHisC Duronio lab N/A Dendra2-H3.3-N-14 Davidson lab Addgene Plasmid #57725 pMBAC-1xHisC-H3-Dendra2 This paper N/A pU6-BbsI-chiRNA Harrison Lab, O’Connor-Giles Lab, Wildonger Lab Addgene Plasmid #45946 pScarlessHD-sfGFP-DsRed O’Connor-Giles Lab Addgene plasmid #80811 pU6-H3.3A-gRNA This paper N/A pScarlessHD-H3.3A-Dendra2-DsRed This paper N/A Software and Algorithms Fiji Open source https://fiji.sc/ Image Lab Bio-Rad http://www.bio-rad.com/en-us/product/ image-lab-software?ID=KRE6P5E8Z ..

    Magnetic Beads:

    Article Title: The phosphodiesterase 2A controls lymphatic junctional maturation via cGMP-dependent notch signaling.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines HDLECs PromoCell Cat# C-12216 HUVECs PromoCell Cat# C-12203 mECs This manuscript N/A Experimental models: Organisms/strains Mouse: Tie2-Cre (B6.Cg-Tg(Tek-cre) 1Ywa/J) Kisanuki et al.69 RRID:IMSR_JAX:008863 Mouse: Cdh5-CreERT2 (Tg(Cdh5-cre/ ERT2)1Rha) Sörensen et al.70 RRID:IMSR_EM:14891 Mouse: Prox1-CreERT2 (Tg(Prox1-cre/ ERT2)1Tmak Bazigou et al.71 RRID:IMSR_EM:13737 Mouse: Pde2a global knockout (B6; 129P2487Pde2A < tm1Dgen>/H; EM: 02366) Assenza et al.25 RRID:IMSR_EM:02366 Mouse: Pde2a (Pde2atm1a(EUCOMM)Wtsl) This manuscript N/A Oligonucleotides AllStars Negative CTRL siRNA Qiagen Cat# 1027281 FlexiTube PDE2A siRNA Qiagen Cat# SI00040159 DLL1 (hs00194509_m1) Thermo Fischer Scientific Cat# 4331182 GAPDH (hs99999905) Thermo Fischer Scientific Cat# 4326317E Gapdh (mm99999915_g1) Thermo Fischer Scientific Cat# 4352932E GJA4 (hs00704917_s1) Thermo Fischer Scientific Cat# 4331182 Hey1 (mm00468865_m1) Thermo Fischer Scientific Cat# 4331182 miR-139-5p (MI0000693) Thermo Fischer Scientific Cat# 002289 Mki67 (mm01278617_m1) Thermo Fischer Scientific Cat# 4331182 PDE10A (hs01098928_m1) Thermo Fischer Scientific Cat# 4351372 PDE12 (hs00698272_m1) Thermo Fischer Scientific Cat# 4331182 PDE2A (hs00159935_m1) Thermo Fischer Scientific Cat# 4331182 Pde2a (mm01136644_m1) Thermo Fischer Scientific Cat# 4331182 PDE3A (hs01012698_m1) Thermo Fischer Scientific Cat# 4331182 PDE4B (hs00963643_m1) Thermo Fischer Scientific Cat# 4331182 PDE4D (hs01579625_m1) Thermo Fischer Scientific Cat# 4331182 PDE6D (hs01062025_m1) Thermo Fischer Scientific Cat# 4331182 PDE8A (hs01079617_m1) Thermo Fischer Scientific Cat# 4331182 PSEN2 (hs01577197_m1) Thermo Fischer Scientific Cat# 4331182 RNU48 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001006 snoRNA202 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001232 snoRNA234 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001234 Pde2a-5’-arm 50ACTGGTCAGTTCTGAGC CTCACCC 30 This paper N/A Pde2a-3’-arm 50 AGTCTGGACTCCCCA TCTAGCAGG 30 This paper N/A Cre transgene sense 50GAACCTGATGG ACATGTTCAGG 30 This paper N/A Cre transgene antisense 50 AGTGCGTT CGAACGCTAGAGCCTGT 30 This paper N/A Myogenin sense 50 TTACGTCCA TCGTGGACAGC 30 This paper N/A Myogenin antisense 50 TGGGCTGGGT GTTAGCCTTA 30 This paper N/A (Continued on next page) e4 Developmental Cell 59, 1–18.e1–e11, February 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms BioRad Image Lab Software BioRad N/A Diva 8.0.1 software BD Biosciences N/A Fiji ImageJ N/A https://imagej.net/ij/ GraphPad Prism 9 Dotmatics N/A Leica LAS-X software Leica N/A MicroManager 1.4 software Open source N/A Seurat package Satija et al.72 https://www.nature.com/articles/nbt.3192 umap package McInnes et al.73 https://joss.theoj.org/papers/10.21105/ joss.00861 Plotly software Open source https://plotly.com/r/ FastQC (v0.11.9) Open source http://www.bioinformatics.babraham.ac. uk/projects/fastqc/ Trimmomatic (v0.36) Bolger et al.74 https://academic.oup.com/bioinformatics/ article/30/15/2114/2390096?login=true STAR (v2.7.3a) Dobin et al.75 https://academic.oup.com/bioinformatics/ article/29/1/15/272537 ComBat-seq Zhang et al.76 https://academic.oup.com/nargab/article/ 2/3/lqaa078/5909519?searchresult=1 WebGestalt platform 2019 Liao et al.77 https://academic.oup.com/nar/article/47/ W1/W199/5494758?login=true Other 24-well Plate Softwell Easy Coat hydrogels (0.1, 1, 2, 4 and 25kPa) Matrigen Cat# SS24-EC 8-well Lab-Tek II chamber slides Lab-Tek Cat# 154941 Agilent Technologies 2100 bioanalyzer Agilent https://www.agilent.com/en/product/ automated-electrophoresis/bioanalyzersystems/bioanalyzer-instrument AMPure XP magnetic beads Beckman Cat# A53880 Axiocam 208 Color Zeiss N/A BD Biosciences FACSAria IIIu BD Biosciences N/A CoolLED beam-splitter DV2 Dual View Photometrics N/A CMOS camera chip OptiMOS, Qimaging N/A DEAE-Sephadex A-25 columns Cytiva Cat# 17017001 DynaMag -2 Invitrogen Cat# 12321D Gel Doc MP Imaging System BioRad N/A Hamilton TLC syringe Sigma-Aldrich Cat# HAM7635-01-1EA Immobilion -P Transfer Membrane (0.45mm pore size) Merck Cat# IPVH00010 Inject -F syringe Braun Cat# 9166017V Leica DMI 3000 B inverted fluorescent microscope Leica N/A Leica SP8 inverted microscope Leica N/A Nikon Eclipse Ts2R microscope Nikon N/A Sheep-anti-rat IgG Dynabeads Invitrogen Cat# 110-35 StepOnePlus RT PCR system Applied Biosystems N/A Tecan Spark 10M microplate reader Tecan N/A Tissue culture-treated dishes Corning Cat# 430167 Tissue culture-treated dishes (60mm) Corning Cat# 430166 Transwell filters (0.4mm pore size) Corning Cat# 3413 (Continued on next page) Developmental Cell 59, 1–18.e1–e11, February 5, 2024 e5 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tri-Carb 2100TR Liquid Scintillation Counter Packard Instruments Cat# 2000CA ULTIMA GOLD scintillation liquid PerkinElmer Cat# 6013326 UltraComp eBeads Plus Compensation Beads Invitrogen Cat# 01-3333-42 Zeiss Stemi 508 Zeiss N/A

    Imaging:

    Article Title: The phosphodiesterase 2A controls lymphatic junctional maturation via cGMP-dependent notch signaling.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines HDLECs PromoCell Cat# C-12216 HUVECs PromoCell Cat# C-12203 mECs This manuscript N/A Experimental models: Organisms/strains Mouse: Tie2-Cre (B6.Cg-Tg(Tek-cre) 1Ywa/J) Kisanuki et al.69 RRID:IMSR_JAX:008863 Mouse: Cdh5-CreERT2 (Tg(Cdh5-cre/ ERT2)1Rha) Sörensen et al.70 RRID:IMSR_EM:14891 Mouse: Prox1-CreERT2 (Tg(Prox1-cre/ ERT2)1Tmak Bazigou et al.71 RRID:IMSR_EM:13737 Mouse: Pde2a global knockout (B6; 129P2487Pde2A < tm1Dgen>/H; EM: 02366) Assenza et al.25 RRID:IMSR_EM:02366 Mouse: Pde2a (Pde2atm1a(EUCOMM)Wtsl) This manuscript N/A Oligonucleotides AllStars Negative CTRL siRNA Qiagen Cat# 1027281 FlexiTube PDE2A siRNA Qiagen Cat# SI00040159 DLL1 (hs00194509_m1) Thermo Fischer Scientific Cat# 4331182 GAPDH (hs99999905) Thermo Fischer Scientific Cat# 4326317E Gapdh (mm99999915_g1) Thermo Fischer Scientific Cat# 4352932E GJA4 (hs00704917_s1) Thermo Fischer Scientific Cat# 4331182 Hey1 (mm00468865_m1) Thermo Fischer Scientific Cat# 4331182 miR-139-5p (MI0000693) Thermo Fischer Scientific Cat# 002289 Mki67 (mm01278617_m1) Thermo Fischer Scientific Cat# 4331182 PDE10A (hs01098928_m1) Thermo Fischer Scientific Cat# 4351372 PDE12 (hs00698272_m1) Thermo Fischer Scientific Cat# 4331182 PDE2A (hs00159935_m1) Thermo Fischer Scientific Cat# 4331182 Pde2a (mm01136644_m1) Thermo Fischer Scientific Cat# 4331182 PDE3A (hs01012698_m1) Thermo Fischer Scientific Cat# 4331182 PDE4B (hs00963643_m1) Thermo Fischer Scientific Cat# 4331182 PDE4D (hs01579625_m1) Thermo Fischer Scientific Cat# 4331182 PDE6D (hs01062025_m1) Thermo Fischer Scientific Cat# 4331182 PDE8A (hs01079617_m1) Thermo Fischer Scientific Cat# 4331182 PSEN2 (hs01577197_m1) Thermo Fischer Scientific Cat# 4331182 RNU48 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001006 snoRNA202 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001232 snoRNA234 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001234 Pde2a-5’-arm 50ACTGGTCAGTTCTGAGC CTCACCC 30 This paper N/A Pde2a-3’-arm 50 AGTCTGGACTCCCCA TCTAGCAGG 30 This paper N/A Cre transgene sense 50GAACCTGATGG ACATGTTCAGG 30 This paper N/A Cre transgene antisense 50 AGTGCGTT CGAACGCTAGAGCCTGT 30 This paper N/A Myogenin sense 50 TTACGTCCA TCGTGGACAGC 30 This paper N/A Myogenin antisense 50 TGGGCTGGGT GTTAGCCTTA 30 This paper N/A (Continued on next page) e4 Developmental Cell 59, 1–18.e1–e11, February 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms BioRad Image Lab Software BioRad N/A Diva 8.0.1 software BD Biosciences N/A Fiji ImageJ N/A https://imagej.net/ij/ GraphPad Prism 9 Dotmatics N/A Leica LAS-X software Leica N/A MicroManager 1.4 software Open source N/A Seurat package Satija et al.72 https://www.nature.com/articles/nbt.3192 umap package McInnes et al.73 https://joss.theoj.org/papers/10.21105/ joss.00861 Plotly software Open source https://plotly.com/r/ FastQC (v0.11.9) Open source http://www.bioinformatics.babraham.ac. uk/projects/fastqc/ Trimmomatic (v0.36) Bolger et al.74 https://academic.oup.com/bioinformatics/ article/30/15/2114/2390096?login=true STAR (v2.7.3a) Dobin et al.75 https://academic.oup.com/bioinformatics/ article/29/1/15/272537 ComBat-seq Zhang et al.76 https://academic.oup.com/nargab/article/ 2/3/lqaa078/5909519?searchresult=1 WebGestalt platform 2019 Liao et al.77 https://academic.oup.com/nar/article/47/ W1/W199/5494758?login=true Other 24-well Plate Softwell Easy Coat hydrogels (0.1, 1, 2, 4 and 25kPa) Matrigen Cat# SS24-EC 8-well Lab-Tek II chamber slides Lab-Tek Cat# 154941 Agilent Technologies 2100 bioanalyzer Agilent https://www.agilent.com/en/product/ automated-electrophoresis/bioanalyzersystems/bioanalyzer-instrument AMPure XP magnetic beads Beckman Cat# A53880 Axiocam 208 Color Zeiss N/A BD Biosciences FACSAria IIIu BD Biosciences N/A CoolLED beam-splitter DV2 Dual View Photometrics N/A CMOS camera chip OptiMOS, Qimaging N/A DEAE-Sephadex A-25 columns Cytiva Cat# 17017001 DynaMag -2 Invitrogen Cat# 12321D Gel Doc MP Imaging System BioRad N/A Hamilton TLC syringe Sigma-Aldrich Cat# HAM7635-01-1EA Immobilion -P Transfer Membrane (0.45mm pore size) Merck Cat# IPVH00010 Inject -F syringe Braun Cat# 9166017V Leica DMI 3000 B inverted fluorescent microscope Leica N/A Leica SP8 inverted microscope Leica N/A Nikon Eclipse Ts2R microscope Nikon N/A Sheep-anti-rat IgG Dynabeads Invitrogen Cat# 110-35 StepOnePlus RT PCR system Applied Biosystems N/A Tecan Spark 10M microplate reader Tecan N/A Tissue culture-treated dishes Corning Cat# 430167 Tissue culture-treated dishes (60mm) Corning Cat# 430166 Transwell filters (0.4mm pore size) Corning Cat# 3413 (Continued on next page) Developmental Cell 59, 1–18.e1–e11, February 5, 2024 e5 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tri-Carb 2100TR Liquid Scintillation Counter Packard Instruments Cat# 2000CA ULTIMA GOLD scintillation liquid PerkinElmer Cat# 6013326 UltraComp eBeads Plus Compensation Beads Invitrogen Cat# 01-3333-42 Zeiss Stemi 508 Zeiss N/A

    Thin Layer Chromatography:

    Article Title: The phosphodiesterase 2A controls lymphatic junctional maturation via cGMP-dependent notch signaling.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines HDLECs PromoCell Cat# C-12216 HUVECs PromoCell Cat# C-12203 mECs This manuscript N/A Experimental models: Organisms/strains Mouse: Tie2-Cre (B6.Cg-Tg(Tek-cre) 1Ywa/J) Kisanuki et al.69 RRID:IMSR_JAX:008863 Mouse: Cdh5-CreERT2 (Tg(Cdh5-cre/ ERT2)1Rha) Sörensen et al.70 RRID:IMSR_EM:14891 Mouse: Prox1-CreERT2 (Tg(Prox1-cre/ ERT2)1Tmak Bazigou et al.71 RRID:IMSR_EM:13737 Mouse: Pde2a global knockout (B6; 129P2487Pde2A < tm1Dgen>/H; EM: 02366) Assenza et al.25 RRID:IMSR_EM:02366 Mouse: Pde2a (Pde2atm1a(EUCOMM)Wtsl) This manuscript N/A Oligonucleotides AllStars Negative CTRL siRNA Qiagen Cat# 1027281 FlexiTube PDE2A siRNA Qiagen Cat# SI00040159 DLL1 (hs00194509_m1) Thermo Fischer Scientific Cat# 4331182 GAPDH (hs99999905) Thermo Fischer Scientific Cat# 4326317E Gapdh (mm99999915_g1) Thermo Fischer Scientific Cat# 4352932E GJA4 (hs00704917_s1) Thermo Fischer Scientific Cat# 4331182 Hey1 (mm00468865_m1) Thermo Fischer Scientific Cat# 4331182 miR-139-5p (MI0000693) Thermo Fischer Scientific Cat# 002289 Mki67 (mm01278617_m1) Thermo Fischer Scientific Cat# 4331182 PDE10A (hs01098928_m1) Thermo Fischer Scientific Cat# 4351372 PDE12 (hs00698272_m1) Thermo Fischer Scientific Cat# 4331182 PDE2A (hs00159935_m1) Thermo Fischer Scientific Cat# 4331182 Pde2a (mm01136644_m1) Thermo Fischer Scientific Cat# 4331182 PDE3A (hs01012698_m1) Thermo Fischer Scientific Cat# 4331182 PDE4B (hs00963643_m1) Thermo Fischer Scientific Cat# 4331182 PDE4D (hs01579625_m1) Thermo Fischer Scientific Cat# 4331182 PDE6D (hs01062025_m1) Thermo Fischer Scientific Cat# 4331182 PDE8A (hs01079617_m1) Thermo Fischer Scientific Cat# 4331182 PSEN2 (hs01577197_m1) Thermo Fischer Scientific Cat# 4331182 RNU48 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001006 snoRNA202 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001232 snoRNA234 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001234 Pde2a-5’-arm 50ACTGGTCAGTTCTGAGC CTCACCC 30 This paper N/A Pde2a-3’-arm 50 AGTCTGGACTCCCCA TCTAGCAGG 30 This paper N/A Cre transgene sense 50GAACCTGATGG ACATGTTCAGG 30 This paper N/A Cre transgene antisense 50 AGTGCGTT CGAACGCTAGAGCCTGT 30 This paper N/A Myogenin sense 50 TTACGTCCA TCGTGGACAGC 30 This paper N/A Myogenin antisense 50 TGGGCTGGGT GTTAGCCTTA 30 This paper N/A (Continued on next page) e4 Developmental Cell 59, 1–18.e1–e11, February 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms BioRad Image Lab Software BioRad N/A Diva 8.0.1 software BD Biosciences N/A Fiji ImageJ N/A https://imagej.net/ij/ GraphPad Prism 9 Dotmatics N/A Leica LAS-X software Leica N/A MicroManager 1.4 software Open source N/A Seurat package Satija et al.72 https://www.nature.com/articles/nbt.3192 umap package McInnes et al.73 https://joss.theoj.org/papers/10.21105/ joss.00861 Plotly software Open source https://plotly.com/r/ FastQC (v0.11.9) Open source http://www.bioinformatics.babraham.ac. uk/projects/fastqc/ Trimmomatic (v0.36) Bolger et al.74 https://academic.oup.com/bioinformatics/ article/30/15/2114/2390096?login=true STAR (v2.7.3a) Dobin et al.75 https://academic.oup.com/bioinformatics/ article/29/1/15/272537 ComBat-seq Zhang et al.76 https://academic.oup.com/nargab/article/ 2/3/lqaa078/5909519?searchresult=1 WebGestalt platform 2019 Liao et al.77 https://academic.oup.com/nar/article/47/ W1/W199/5494758?login=true Other 24-well Plate Softwell Easy Coat hydrogels (0.1, 1, 2, 4 and 25kPa) Matrigen Cat# SS24-EC 8-well Lab-Tek II chamber slides Lab-Tek Cat# 154941 Agilent Technologies 2100 bioanalyzer Agilent https://www.agilent.com/en/product/ automated-electrophoresis/bioanalyzersystems/bioanalyzer-instrument AMPure XP magnetic beads Beckman Cat# A53880 Axiocam 208 Color Zeiss N/A BD Biosciences FACSAria IIIu BD Biosciences N/A CoolLED beam-splitter DV2 Dual View Photometrics N/A CMOS camera chip OptiMOS, Qimaging N/A DEAE-Sephadex A-25 columns Cytiva Cat# 17017001 DynaMag -2 Invitrogen Cat# 12321D Gel Doc MP Imaging System BioRad N/A Hamilton TLC syringe Sigma-Aldrich Cat# HAM7635-01-1EA Immobilion -P Transfer Membrane (0.45mm pore size) Merck Cat# IPVH00010 Inject -F syringe Braun Cat# 9166017V Leica DMI 3000 B inverted fluorescent microscope Leica N/A Leica SP8 inverted microscope Leica N/A Nikon Eclipse Ts2R microscope Nikon N/A Sheep-anti-rat IgG Dynabeads Invitrogen Cat# 110-35 StepOnePlus RT PCR system Applied Biosystems N/A Tecan Spark 10M microplate reader Tecan N/A Tissue culture-treated dishes Corning Cat# 430167 Tissue culture-treated dishes (60mm) Corning Cat# 430166 Transwell filters (0.4mm pore size) Corning Cat# 3413 (Continued on next page) Developmental Cell 59, 1–18.e1–e11, February 5, 2024 e5 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tri-Carb 2100TR Liquid Scintillation Counter Packard Instruments Cat# 2000CA ULTIMA GOLD scintillation liquid PerkinElmer Cat# 6013326 UltraComp eBeads Plus Compensation Beads Invitrogen Cat# 01-3333-42 Zeiss Stemi 508 Zeiss N/A

    Membrane:

    Article Title: The phosphodiesterase 2A controls lymphatic junctional maturation via cGMP-dependent notch signaling.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines HDLECs PromoCell Cat# C-12216 HUVECs PromoCell Cat# C-12203 mECs This manuscript N/A Experimental models: Organisms/strains Mouse: Tie2-Cre (B6.Cg-Tg(Tek-cre) 1Ywa/J) Kisanuki et al.69 RRID:IMSR_JAX:008863 Mouse: Cdh5-CreERT2 (Tg(Cdh5-cre/ ERT2)1Rha) Sörensen et al.70 RRID:IMSR_EM:14891 Mouse: Prox1-CreERT2 (Tg(Prox1-cre/ ERT2)1Tmak Bazigou et al.71 RRID:IMSR_EM:13737 Mouse: Pde2a global knockout (B6; 129P2487Pde2A < tm1Dgen>/H; EM: 02366) Assenza et al.25 RRID:IMSR_EM:02366 Mouse: Pde2a (Pde2atm1a(EUCOMM)Wtsl) This manuscript N/A Oligonucleotides AllStars Negative CTRL siRNA Qiagen Cat# 1027281 FlexiTube PDE2A siRNA Qiagen Cat# SI00040159 DLL1 (hs00194509_m1) Thermo Fischer Scientific Cat# 4331182 GAPDH (hs99999905) Thermo Fischer Scientific Cat# 4326317E Gapdh (mm99999915_g1) Thermo Fischer Scientific Cat# 4352932E GJA4 (hs00704917_s1) Thermo Fischer Scientific Cat# 4331182 Hey1 (mm00468865_m1) Thermo Fischer Scientific Cat# 4331182 miR-139-5p (MI0000693) Thermo Fischer Scientific Cat# 002289 Mki67 (mm01278617_m1) Thermo Fischer Scientific Cat# 4331182 PDE10A (hs01098928_m1) Thermo Fischer Scientific Cat# 4351372 PDE12 (hs00698272_m1) Thermo Fischer Scientific Cat# 4331182 PDE2A (hs00159935_m1) Thermo Fischer Scientific Cat# 4331182 Pde2a (mm01136644_m1) Thermo Fischer Scientific Cat# 4331182 PDE3A (hs01012698_m1) Thermo Fischer Scientific Cat# 4331182 PDE4B (hs00963643_m1) Thermo Fischer Scientific Cat# 4331182 PDE4D (hs01579625_m1) Thermo Fischer Scientific Cat# 4331182 PDE6D (hs01062025_m1) Thermo Fischer Scientific Cat# 4331182 PDE8A (hs01079617_m1) Thermo Fischer Scientific Cat# 4331182 PSEN2 (hs01577197_m1) Thermo Fischer Scientific Cat# 4331182 RNU48 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001006 snoRNA202 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001232 snoRNA234 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001234 Pde2a-5’-arm 50ACTGGTCAGTTCTGAGC CTCACCC 30 This paper N/A Pde2a-3’-arm 50 AGTCTGGACTCCCCA TCTAGCAGG 30 This paper N/A Cre transgene sense 50GAACCTGATGG ACATGTTCAGG 30 This paper N/A Cre transgene antisense 50 AGTGCGTT CGAACGCTAGAGCCTGT 30 This paper N/A Myogenin sense 50 TTACGTCCA TCGTGGACAGC 30 This paper N/A Myogenin antisense 50 TGGGCTGGGT GTTAGCCTTA 30 This paper N/A (Continued on next page) e4 Developmental Cell 59, 1–18.e1–e11, February 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms BioRad Image Lab Software BioRad N/A Diva 8.0.1 software BD Biosciences N/A Fiji ImageJ N/A https://imagej.net/ij/ GraphPad Prism 9 Dotmatics N/A Leica LAS-X software Leica N/A MicroManager 1.4 software Open source N/A Seurat package Satija et al.72 https://www.nature.com/articles/nbt.3192 umap package McInnes et al.73 https://joss.theoj.org/papers/10.21105/ joss.00861 Plotly software Open source https://plotly.com/r/ FastQC (v0.11.9) Open source http://www.bioinformatics.babraham.ac. uk/projects/fastqc/ Trimmomatic (v0.36) Bolger et al.74 https://academic.oup.com/bioinformatics/ article/30/15/2114/2390096?login=true STAR (v2.7.3a) Dobin et al.75 https://academic.oup.com/bioinformatics/ article/29/1/15/272537 ComBat-seq Zhang et al.76 https://academic.oup.com/nargab/article/ 2/3/lqaa078/5909519?searchresult=1 WebGestalt platform 2019 Liao et al.77 https://academic.oup.com/nar/article/47/ W1/W199/5494758?login=true Other 24-well Plate Softwell Easy Coat hydrogels (0.1, 1, 2, 4 and 25kPa) Matrigen Cat# SS24-EC 8-well Lab-Tek II chamber slides Lab-Tek Cat# 154941 Agilent Technologies 2100 bioanalyzer Agilent https://www.agilent.com/en/product/ automated-electrophoresis/bioanalyzersystems/bioanalyzer-instrument AMPure XP magnetic beads Beckman Cat# A53880 Axiocam 208 Color Zeiss N/A BD Biosciences FACSAria IIIu BD Biosciences N/A CoolLED beam-splitter DV2 Dual View Photometrics N/A CMOS camera chip OptiMOS, Qimaging N/A DEAE-Sephadex A-25 columns Cytiva Cat# 17017001 DynaMag -2 Invitrogen Cat# 12321D Gel Doc MP Imaging System BioRad N/A Hamilton TLC syringe Sigma-Aldrich Cat# HAM7635-01-1EA Immobilion -P Transfer Membrane (0.45mm pore size) Merck Cat# IPVH00010 Inject -F syringe Braun Cat# 9166017V Leica DMI 3000 B inverted fluorescent microscope Leica N/A Leica SP8 inverted microscope Leica N/A Nikon Eclipse Ts2R microscope Nikon N/A Sheep-anti-rat IgG Dynabeads Invitrogen Cat# 110-35 StepOnePlus RT PCR system Applied Biosystems N/A Tecan Spark 10M microplate reader Tecan N/A Tissue culture-treated dishes Corning Cat# 430167 Tissue culture-treated dishes (60mm) Corning Cat# 430166 Transwell filters (0.4mm pore size) Corning Cat# 3413 (Continued on next page) Developmental Cell 59, 1–18.e1–e11, February 5, 2024 e5 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tri-Carb 2100TR Liquid Scintillation Counter Packard Instruments Cat# 2000CA ULTIMA GOLD scintillation liquid PerkinElmer Cat# 6013326 UltraComp eBeads Plus Compensation Beads Invitrogen Cat# 01-3333-42 Zeiss Stemi 508 Zeiss N/A

    Pore Size:

    Article Title: The phosphodiesterase 2A controls lymphatic junctional maturation via cGMP-dependent notch signaling.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines HDLECs PromoCell Cat# C-12216 HUVECs PromoCell Cat# C-12203 mECs This manuscript N/A Experimental models: Organisms/strains Mouse: Tie2-Cre (B6.Cg-Tg(Tek-cre) 1Ywa/J) Kisanuki et al.69 RRID:IMSR_JAX:008863 Mouse: Cdh5-CreERT2 (Tg(Cdh5-cre/ ERT2)1Rha) Sörensen et al.70 RRID:IMSR_EM:14891 Mouse: Prox1-CreERT2 (Tg(Prox1-cre/ ERT2)1Tmak Bazigou et al.71 RRID:IMSR_EM:13737 Mouse: Pde2a global knockout (B6; 129P2487Pde2A < tm1Dgen>/H; EM: 02366) Assenza et al.25 RRID:IMSR_EM:02366 Mouse: Pde2a (Pde2atm1a(EUCOMM)Wtsl) This manuscript N/A Oligonucleotides AllStars Negative CTRL siRNA Qiagen Cat# 1027281 FlexiTube PDE2A siRNA Qiagen Cat# SI00040159 DLL1 (hs00194509_m1) Thermo Fischer Scientific Cat# 4331182 GAPDH (hs99999905) Thermo Fischer Scientific Cat# 4326317E Gapdh (mm99999915_g1) Thermo Fischer Scientific Cat# 4352932E GJA4 (hs00704917_s1) Thermo Fischer Scientific Cat# 4331182 Hey1 (mm00468865_m1) Thermo Fischer Scientific Cat# 4331182 miR-139-5p (MI0000693) Thermo Fischer Scientific Cat# 002289 Mki67 (mm01278617_m1) Thermo Fischer Scientific Cat# 4331182 PDE10A (hs01098928_m1) Thermo Fischer Scientific Cat# 4351372 PDE12 (hs00698272_m1) Thermo Fischer Scientific Cat# 4331182 PDE2A (hs00159935_m1) Thermo Fischer Scientific Cat# 4331182 Pde2a (mm01136644_m1) Thermo Fischer Scientific Cat# 4331182 PDE3A (hs01012698_m1) Thermo Fischer Scientific Cat# 4331182 PDE4B (hs00963643_m1) Thermo Fischer Scientific Cat# 4331182 PDE4D (hs01579625_m1) Thermo Fischer Scientific Cat# 4331182 PDE6D (hs01062025_m1) Thermo Fischer Scientific Cat# 4331182 PDE8A (hs01079617_m1) Thermo Fischer Scientific Cat# 4331182 PSEN2 (hs01577197_m1) Thermo Fischer Scientific Cat# 4331182 RNU48 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001006 snoRNA202 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001232 snoRNA234 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001234 Pde2a-5’-arm 50ACTGGTCAGTTCTGAGC CTCACCC 30 This paper N/A Pde2a-3’-arm 50 AGTCTGGACTCCCCA TCTAGCAGG 30 This paper N/A Cre transgene sense 50GAACCTGATGG ACATGTTCAGG 30 This paper N/A Cre transgene antisense 50 AGTGCGTT CGAACGCTAGAGCCTGT 30 This paper N/A Myogenin sense 50 TTACGTCCA TCGTGGACAGC 30 This paper N/A Myogenin antisense 50 TGGGCTGGGT GTTAGCCTTA 30 This paper N/A (Continued on next page) e4 Developmental Cell 59, 1–18.e1–e11, February 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms BioRad Image Lab Software BioRad N/A Diva 8.0.1 software BD Biosciences N/A Fiji ImageJ N/A https://imagej.net/ij/ GraphPad Prism 9 Dotmatics N/A Leica LAS-X software Leica N/A MicroManager 1.4 software Open source N/A Seurat package Satija et al.72 https://www.nature.com/articles/nbt.3192 umap package McInnes et al.73 https://joss.theoj.org/papers/10.21105/ joss.00861 Plotly software Open source https://plotly.com/r/ FastQC (v0.11.9) Open source http://www.bioinformatics.babraham.ac. uk/projects/fastqc/ Trimmomatic (v0.36) Bolger et al.74 https://academic.oup.com/bioinformatics/ article/30/15/2114/2390096?login=true STAR (v2.7.3a) Dobin et al.75 https://academic.oup.com/bioinformatics/ article/29/1/15/272537 ComBat-seq Zhang et al.76 https://academic.oup.com/nargab/article/ 2/3/lqaa078/5909519?searchresult=1 WebGestalt platform 2019 Liao et al.77 https://academic.oup.com/nar/article/47/ W1/W199/5494758?login=true Other 24-well Plate Softwell Easy Coat hydrogels (0.1, 1, 2, 4 and 25kPa) Matrigen Cat# SS24-EC 8-well Lab-Tek II chamber slides Lab-Tek Cat# 154941 Agilent Technologies 2100 bioanalyzer Agilent https://www.agilent.com/en/product/ automated-electrophoresis/bioanalyzersystems/bioanalyzer-instrument AMPure XP magnetic beads Beckman Cat# A53880 Axiocam 208 Color Zeiss N/A BD Biosciences FACSAria IIIu BD Biosciences N/A CoolLED beam-splitter DV2 Dual View Photometrics N/A CMOS camera chip OptiMOS, Qimaging N/A DEAE-Sephadex A-25 columns Cytiva Cat# 17017001 DynaMag -2 Invitrogen Cat# 12321D Gel Doc MP Imaging System BioRad N/A Hamilton TLC syringe Sigma-Aldrich Cat# HAM7635-01-1EA Immobilion -P Transfer Membrane (0.45mm pore size) Merck Cat# IPVH00010 Inject -F syringe Braun Cat# 9166017V Leica DMI 3000 B inverted fluorescent microscope Leica N/A Leica SP8 inverted microscope Leica N/A Nikon Eclipse Ts2R microscope Nikon N/A Sheep-anti-rat IgG Dynabeads Invitrogen Cat# 110-35 StepOnePlus RT PCR system Applied Biosystems N/A Tecan Spark 10M microplate reader Tecan N/A Tissue culture-treated dishes Corning Cat# 430167 Tissue culture-treated dishes (60mm) Corning Cat# 430166 Transwell filters (0.4mm pore size) Corning Cat# 3413 (Continued on next page) Developmental Cell 59, 1–18.e1–e11, February 5, 2024 e5 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tri-Carb 2100TR Liquid Scintillation Counter Packard Instruments Cat# 2000CA ULTIMA GOLD scintillation liquid PerkinElmer Cat# 6013326 UltraComp eBeads Plus Compensation Beads Invitrogen Cat# 01-3333-42 Zeiss Stemi 508 Zeiss N/A

    Microscopy:

    Article Title: The phosphodiesterase 2A controls lymphatic junctional maturation via cGMP-dependent notch signaling.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines HDLECs PromoCell Cat# C-12216 HUVECs PromoCell Cat# C-12203 mECs This manuscript N/A Experimental models: Organisms/strains Mouse: Tie2-Cre (B6.Cg-Tg(Tek-cre) 1Ywa/J) Kisanuki et al.69 RRID:IMSR_JAX:008863 Mouse: Cdh5-CreERT2 (Tg(Cdh5-cre/ ERT2)1Rha) Sörensen et al.70 RRID:IMSR_EM:14891 Mouse: Prox1-CreERT2 (Tg(Prox1-cre/ ERT2)1Tmak Bazigou et al.71 RRID:IMSR_EM:13737 Mouse: Pde2a global knockout (B6; 129P2487Pde2A < tm1Dgen>/H; EM: 02366) Assenza et al.25 RRID:IMSR_EM:02366 Mouse: Pde2a (Pde2atm1a(EUCOMM)Wtsl) This manuscript N/A Oligonucleotides AllStars Negative CTRL siRNA Qiagen Cat# 1027281 FlexiTube PDE2A siRNA Qiagen Cat# SI00040159 DLL1 (hs00194509_m1) Thermo Fischer Scientific Cat# 4331182 GAPDH (hs99999905) Thermo Fischer Scientific Cat# 4326317E Gapdh (mm99999915_g1) Thermo Fischer Scientific Cat# 4352932E GJA4 (hs00704917_s1) Thermo Fischer Scientific Cat# 4331182 Hey1 (mm00468865_m1) Thermo Fischer Scientific Cat# 4331182 miR-139-5p (MI0000693) Thermo Fischer Scientific Cat# 002289 Mki67 (mm01278617_m1) Thermo Fischer Scientific Cat# 4331182 PDE10A (hs01098928_m1) Thermo Fischer Scientific Cat# 4351372 PDE12 (hs00698272_m1) Thermo Fischer Scientific Cat# 4331182 PDE2A (hs00159935_m1) Thermo Fischer Scientific Cat# 4331182 Pde2a (mm01136644_m1) Thermo Fischer Scientific Cat# 4331182 PDE3A (hs01012698_m1) Thermo Fischer Scientific Cat# 4331182 PDE4B (hs00963643_m1) Thermo Fischer Scientific Cat# 4331182 PDE4D (hs01579625_m1) Thermo Fischer Scientific Cat# 4331182 PDE6D (hs01062025_m1) Thermo Fischer Scientific Cat# 4331182 PDE8A (hs01079617_m1) Thermo Fischer Scientific Cat# 4331182 PSEN2 (hs01577197_m1) Thermo Fischer Scientific Cat# 4331182 RNU48 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001006 snoRNA202 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001232 snoRNA234 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001234 Pde2a-5’-arm 50ACTGGTCAGTTCTGAGC CTCACCC 30 This paper N/A Pde2a-3’-arm 50 AGTCTGGACTCCCCA TCTAGCAGG 30 This paper N/A Cre transgene sense 50GAACCTGATGG ACATGTTCAGG 30 This paper N/A Cre transgene antisense 50 AGTGCGTT CGAACGCTAGAGCCTGT 30 This paper N/A Myogenin sense 50 TTACGTCCA TCGTGGACAGC 30 This paper N/A Myogenin antisense 50 TGGGCTGGGT GTTAGCCTTA 30 This paper N/A (Continued on next page) e4 Developmental Cell 59, 1–18.e1–e11, February 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms BioRad Image Lab Software BioRad N/A Diva 8.0.1 software BD Biosciences N/A Fiji ImageJ N/A https://imagej.net/ij/ GraphPad Prism 9 Dotmatics N/A Leica LAS-X software Leica N/A MicroManager 1.4 software Open source N/A Seurat package Satija et al.72 https://www.nature.com/articles/nbt.3192 umap package McInnes et al.73 https://joss.theoj.org/papers/10.21105/ joss.00861 Plotly software Open source https://plotly.com/r/ FastQC (v0.11.9) Open source http://www.bioinformatics.babraham.ac. uk/projects/fastqc/ Trimmomatic (v0.36) Bolger et al.74 https://academic.oup.com/bioinformatics/ article/30/15/2114/2390096?login=true STAR (v2.7.3a) Dobin et al.75 https://academic.oup.com/bioinformatics/ article/29/1/15/272537 ComBat-seq Zhang et al.76 https://academic.oup.com/nargab/article/ 2/3/lqaa078/5909519?searchresult=1 WebGestalt platform 2019 Liao et al.77 https://academic.oup.com/nar/article/47/ W1/W199/5494758?login=true Other 24-well Plate Softwell Easy Coat hydrogels (0.1, 1, 2, 4 and 25kPa) Matrigen Cat# SS24-EC 8-well Lab-Tek II chamber slides Lab-Tek Cat# 154941 Agilent Technologies 2100 bioanalyzer Agilent https://www.agilent.com/en/product/ automated-electrophoresis/bioanalyzersystems/bioanalyzer-instrument AMPure XP magnetic beads Beckman Cat# A53880 Axiocam 208 Color Zeiss N/A BD Biosciences FACSAria IIIu BD Biosciences N/A CoolLED beam-splitter DV2 Dual View Photometrics N/A CMOS camera chip OptiMOS, Qimaging N/A DEAE-Sephadex A-25 columns Cytiva Cat# 17017001 DynaMag -2 Invitrogen Cat# 12321D Gel Doc MP Imaging System BioRad N/A Hamilton TLC syringe Sigma-Aldrich Cat# HAM7635-01-1EA Immobilion -P Transfer Membrane (0.45mm pore size) Merck Cat# IPVH00010 Inject -F syringe Braun Cat# 9166017V Leica DMI 3000 B inverted fluorescent microscope Leica N/A Leica SP8 inverted microscope Leica N/A Nikon Eclipse Ts2R microscope Nikon N/A Sheep-anti-rat IgG Dynabeads Invitrogen Cat# 110-35 StepOnePlus RT PCR system Applied Biosystems N/A Tecan Spark 10M microplate reader Tecan N/A Tissue culture-treated dishes Corning Cat# 430167 Tissue culture-treated dishes (60mm) Corning Cat# 430166 Transwell filters (0.4mm pore size) Corning Cat# 3413 (Continued on next page) Developmental Cell 59, 1–18.e1–e11, February 5, 2024 e5 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tri-Carb 2100TR Liquid Scintillation Counter Packard Instruments Cat# 2000CA ULTIMA GOLD scintillation liquid PerkinElmer Cat# 6013326 UltraComp eBeads Plus Compensation Beads Invitrogen Cat# 01-3333-42 Zeiss Stemi 508 Zeiss N/A

    Inverted Microscopy:

    Article Title: The phosphodiesterase 2A controls lymphatic junctional maturation via cGMP-dependent notch signaling.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines HDLECs PromoCell Cat# C-12216 HUVECs PromoCell Cat# C-12203 mECs This manuscript N/A Experimental models: Organisms/strains Mouse: Tie2-Cre (B6.Cg-Tg(Tek-cre) 1Ywa/J) Kisanuki et al.69 RRID:IMSR_JAX:008863 Mouse: Cdh5-CreERT2 (Tg(Cdh5-cre/ ERT2)1Rha) Sörensen et al.70 RRID:IMSR_EM:14891 Mouse: Prox1-CreERT2 (Tg(Prox1-cre/ ERT2)1Tmak Bazigou et al.71 RRID:IMSR_EM:13737 Mouse: Pde2a global knockout (B6; 129P2487Pde2A < tm1Dgen>/H; EM: 02366) Assenza et al.25 RRID:IMSR_EM:02366 Mouse: Pde2a (Pde2atm1a(EUCOMM)Wtsl) This manuscript N/A Oligonucleotides AllStars Negative CTRL siRNA Qiagen Cat# 1027281 FlexiTube PDE2A siRNA Qiagen Cat# SI00040159 DLL1 (hs00194509_m1) Thermo Fischer Scientific Cat# 4331182 GAPDH (hs99999905) Thermo Fischer Scientific Cat# 4326317E Gapdh (mm99999915_g1) Thermo Fischer Scientific Cat# 4352932E GJA4 (hs00704917_s1) Thermo Fischer Scientific Cat# 4331182 Hey1 (mm00468865_m1) Thermo Fischer Scientific Cat# 4331182 miR-139-5p (MI0000693) Thermo Fischer Scientific Cat# 002289 Mki67 (mm01278617_m1) Thermo Fischer Scientific Cat# 4331182 PDE10A (hs01098928_m1) Thermo Fischer Scientific Cat# 4351372 PDE12 (hs00698272_m1) Thermo Fischer Scientific Cat# 4331182 PDE2A (hs00159935_m1) Thermo Fischer Scientific Cat# 4331182 Pde2a (mm01136644_m1) Thermo Fischer Scientific Cat# 4331182 PDE3A (hs01012698_m1) Thermo Fischer Scientific Cat# 4331182 PDE4B (hs00963643_m1) Thermo Fischer Scientific Cat# 4331182 PDE4D (hs01579625_m1) Thermo Fischer Scientific Cat# 4331182 PDE6D (hs01062025_m1) Thermo Fischer Scientific Cat# 4331182 PDE8A (hs01079617_m1) Thermo Fischer Scientific Cat# 4331182 PSEN2 (hs01577197_m1) Thermo Fischer Scientific Cat# 4331182 RNU48 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001006 snoRNA202 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001232 snoRNA234 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001234 Pde2a-5’-arm 50ACTGGTCAGTTCTGAGC CTCACCC 30 This paper N/A Pde2a-3’-arm 50 AGTCTGGACTCCCCA TCTAGCAGG 30 This paper N/A Cre transgene sense 50GAACCTGATGG ACATGTTCAGG 30 This paper N/A Cre transgene antisense 50 AGTGCGTT CGAACGCTAGAGCCTGT 30 This paper N/A Myogenin sense 50 TTACGTCCA TCGTGGACAGC 30 This paper N/A Myogenin antisense 50 TGGGCTGGGT GTTAGCCTTA 30 This paper N/A (Continued on next page) e4 Developmental Cell 59, 1–18.e1–e11, February 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms BioRad Image Lab Software BioRad N/A Diva 8.0.1 software BD Biosciences N/A Fiji ImageJ N/A https://imagej.net/ij/ GraphPad Prism 9 Dotmatics N/A Leica LAS-X software Leica N/A MicroManager 1.4 software Open source N/A Seurat package Satija et al.72 https://www.nature.com/articles/nbt.3192 umap package McInnes et al.73 https://joss.theoj.org/papers/10.21105/ joss.00861 Plotly software Open source https://plotly.com/r/ FastQC (v0.11.9) Open source http://www.bioinformatics.babraham.ac. uk/projects/fastqc/ Trimmomatic (v0.36) Bolger et al.74 https://academic.oup.com/bioinformatics/ article/30/15/2114/2390096?login=true STAR (v2.7.3a) Dobin et al.75 https://academic.oup.com/bioinformatics/ article/29/1/15/272537 ComBat-seq Zhang et al.76 https://academic.oup.com/nargab/article/ 2/3/lqaa078/5909519?searchresult=1 WebGestalt platform 2019 Liao et al.77 https://academic.oup.com/nar/article/47/ W1/W199/5494758?login=true Other 24-well Plate Softwell Easy Coat hydrogels (0.1, 1, 2, 4 and 25kPa) Matrigen Cat# SS24-EC 8-well Lab-Tek II chamber slides Lab-Tek Cat# 154941 Agilent Technologies 2100 bioanalyzer Agilent https://www.agilent.com/en/product/ automated-electrophoresis/bioanalyzersystems/bioanalyzer-instrument AMPure XP magnetic beads Beckman Cat# A53880 Axiocam 208 Color Zeiss N/A BD Biosciences FACSAria IIIu BD Biosciences N/A CoolLED beam-splitter DV2 Dual View Photometrics N/A CMOS camera chip OptiMOS, Qimaging N/A DEAE-Sephadex A-25 columns Cytiva Cat# 17017001 DynaMag -2 Invitrogen Cat# 12321D Gel Doc MP Imaging System BioRad N/A Hamilton TLC syringe Sigma-Aldrich Cat# HAM7635-01-1EA Immobilion -P Transfer Membrane (0.45mm pore size) Merck Cat# IPVH00010 Inject -F syringe Braun Cat# 9166017V Leica DMI 3000 B inverted fluorescent microscope Leica N/A Leica SP8 inverted microscope Leica N/A Nikon Eclipse Ts2R microscope Nikon N/A Sheep-anti-rat IgG Dynabeads Invitrogen Cat# 110-35 StepOnePlus RT PCR system Applied Biosystems N/A Tecan Spark 10M microplate reader Tecan N/A Tissue culture-treated dishes Corning Cat# 430167 Tissue culture-treated dishes (60mm) Corning Cat# 430166 Transwell filters (0.4mm pore size) Corning Cat# 3413 (Continued on next page) Developmental Cell 59, 1–18.e1–e11, February 5, 2024 e5 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tri-Carb 2100TR Liquid Scintillation Counter Packard Instruments Cat# 2000CA ULTIMA GOLD scintillation liquid PerkinElmer Cat# 6013326 UltraComp eBeads Plus Compensation Beads Invitrogen Cat# 01-3333-42 Zeiss Stemi 508 Zeiss N/A

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: The phosphodiesterase 2A controls lymphatic junctional maturation via cGMP-dependent notch signaling.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines HDLECs PromoCell Cat# C-12216 HUVECs PromoCell Cat# C-12203 mECs This manuscript N/A Experimental models: Organisms/strains Mouse: Tie2-Cre (B6.Cg-Tg(Tek-cre) 1Ywa/J) Kisanuki et al.69 RRID:IMSR_JAX:008863 Mouse: Cdh5-CreERT2 (Tg(Cdh5-cre/ ERT2)1Rha) Sörensen et al.70 RRID:IMSR_EM:14891 Mouse: Prox1-CreERT2 (Tg(Prox1-cre/ ERT2)1Tmak Bazigou et al.71 RRID:IMSR_EM:13737 Mouse: Pde2a global knockout (B6; 129P2487Pde2A < tm1Dgen>/H; EM: 02366) Assenza et al.25 RRID:IMSR_EM:02366 Mouse: Pde2a (Pde2atm1a(EUCOMM)Wtsl) This manuscript N/A Oligonucleotides AllStars Negative CTRL siRNA Qiagen Cat# 1027281 FlexiTube PDE2A siRNA Qiagen Cat# SI00040159 DLL1 (hs00194509_m1) Thermo Fischer Scientific Cat# 4331182 GAPDH (hs99999905) Thermo Fischer Scientific Cat# 4326317E Gapdh (mm99999915_g1) Thermo Fischer Scientific Cat# 4352932E GJA4 (hs00704917_s1) Thermo Fischer Scientific Cat# 4331182 Hey1 (mm00468865_m1) Thermo Fischer Scientific Cat# 4331182 miR-139-5p (MI0000693) Thermo Fischer Scientific Cat# 002289 Mki67 (mm01278617_m1) Thermo Fischer Scientific Cat# 4331182 PDE10A (hs01098928_m1) Thermo Fischer Scientific Cat# 4351372 PDE12 (hs00698272_m1) Thermo Fischer Scientific Cat# 4331182 PDE2A (hs00159935_m1) Thermo Fischer Scientific Cat# 4331182 Pde2a (mm01136644_m1) Thermo Fischer Scientific Cat# 4331182 PDE3A (hs01012698_m1) Thermo Fischer Scientific Cat# 4331182 PDE4B (hs00963643_m1) Thermo Fischer Scientific Cat# 4331182 PDE4D (hs01579625_m1) Thermo Fischer Scientific Cat# 4331182 PDE6D (hs01062025_m1) Thermo Fischer Scientific Cat# 4331182 PDE8A (hs01079617_m1) Thermo Fischer Scientific Cat# 4331182 PSEN2 (hs01577197_m1) Thermo Fischer Scientific Cat# 4331182 RNU48 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001006 snoRNA202 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001232 snoRNA234 (TaqMan MicroRNA Assay) Thermo Fischer Scientific Cat# 001234 Pde2a-5’-arm 50ACTGGTCAGTTCTGAGC CTCACCC 30 This paper N/A Pde2a-3’-arm 50 AGTCTGGACTCCCCA TCTAGCAGG 30 This paper N/A Cre transgene sense 50GAACCTGATGG ACATGTTCAGG 30 This paper N/A Cre transgene antisense 50 AGTGCGTT CGAACGCTAGAGCCTGT 30 This paper N/A Myogenin sense 50 TTACGTCCA TCGTGGACAGC 30 This paper N/A Myogenin antisense 50 TGGGCTGGGT GTTAGCCTTA 30 This paper N/A (Continued on next page) e4 Developmental Cell 59, 1–18.e1–e11, February 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms BioRad Image Lab Software BioRad N/A Diva 8.0.1 software BD Biosciences N/A Fiji ImageJ N/A https://imagej.net/ij/ GraphPad Prism 9 Dotmatics N/A Leica LAS-X software Leica N/A MicroManager 1.4 software Open source N/A Seurat package Satija et al.72 https://www.nature.com/articles/nbt.3192 umap package McInnes et al.73 https://joss.theoj.org/papers/10.21105/ joss.00861 Plotly software Open source https://plotly.com/r/ FastQC (v0.11.9) Open source http://www.bioinformatics.babraham.ac. uk/projects/fastqc/ Trimmomatic (v0.36) Bolger et al.74 https://academic.oup.com/bioinformatics/ article/30/15/2114/2390096?login=true STAR (v2.7.3a) Dobin et al.75 https://academic.oup.com/bioinformatics/ article/29/1/15/272537 ComBat-seq Zhang et al.76 https://academic.oup.com/nargab/article/ 2/3/lqaa078/5909519?searchresult=1 WebGestalt platform 2019 Liao et al.77 https://academic.oup.com/nar/article/47/ W1/W199/5494758?login=true Other 24-well Plate Softwell Easy Coat hydrogels (0.1, 1, 2, 4 and 25kPa) Matrigen Cat# SS24-EC 8-well Lab-Tek II chamber slides Lab-Tek Cat# 154941 Agilent Technologies 2100 bioanalyzer Agilent https://www.agilent.com/en/product/ automated-electrophoresis/bioanalyzersystems/bioanalyzer-instrument AMPure XP magnetic beads Beckman Cat# A53880 Axiocam 208 Color Zeiss N/A BD Biosciences FACSAria IIIu BD Biosciences N/A CoolLED beam-splitter DV2 Dual View Photometrics N/A CMOS camera chip OptiMOS, Qimaging N/A DEAE-Sephadex A-25 columns Cytiva Cat# 17017001 DynaMag -2 Invitrogen Cat# 12321D Gel Doc MP Imaging System BioRad N/A Hamilton TLC syringe Sigma-Aldrich Cat# HAM7635-01-1EA Immobilion -P Transfer Membrane (0.45mm pore size) Merck Cat# IPVH00010 Inject -F syringe Braun Cat# 9166017V Leica DMI 3000 B inverted fluorescent microscope Leica N/A Leica SP8 inverted microscope Leica N/A Nikon Eclipse Ts2R microscope Nikon N/A Sheep-anti-rat IgG Dynabeads Invitrogen Cat# 110-35 StepOnePlus RT PCR system Applied Biosystems N/A Tecan Spark 10M microplate reader Tecan N/A Tissue culture-treated dishes Corning Cat# 430167 Tissue culture-treated dishes (60mm) Corning Cat# 430166 Transwell filters (0.4mm pore size) Corning Cat# 3413 (Continued on next page) Developmental Cell 59, 1–18.e1–e11, February 5, 2024 e5 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tri-Carb 2100TR Liquid Scintillation Counter Packard Instruments Cat# 2000CA ULTIMA GOLD scintillation liquid PerkinElmer Cat# 6013326 UltraComp eBeads Plus Compensation Beads Invitrogen Cat# 01-3333-42 Zeiss Stemi 508 Zeiss N/A



    Similar Products

    source software fiji  (Oxford Instruments)
    99
    Oxford Instruments source software fiji
    Source Software Fiji, supplied by Oxford Instruments, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/source+software+fiji/Imaris/pm41544800-51-5-10
    Average 99 stars, based on 1 article reviews
    source software fiji - by Bioz Stars, 2026-09
    99/100 stars
    		  Buy from Supplier
    resource source identifier image j fiji nih  (Bio-Rad)
    99
    Bio-Rad resource source identifier image j fiji nih
    Resource Source Identifier Image J Fiji Nih, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/source+software+fiji/Image+Lab+Software/pm41330383-1014-2-15
    Average 99 stars, based on 1 article reviews
    resource source identifier image j fiji nih - by Bioz Stars, 2026-09
    99/100 stars
    		  Buy from Supplier
    open source fiji software  (Oxford Instruments)
    99
    Oxford Instruments open source fiji software
    Open Source Fiji Software, supplied by Oxford Instruments, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/source+software+fiji/Imaris/bio_rxiv__2025__10__23__684231-316-13-20
    Average 99 stars, based on 1 article reviews
    open source fiji software - by Bioz Stars, 2026-09
    99/100 stars
    		  Buy from Supplier
    source software fiji imagej  (Oxford Instruments)
    99
    Oxford Instruments source software fiji imagej
    Source Software Fiji Imagej, supplied by Oxford Instruments, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/source+software+fiji/Imaris/bio_rxiv__2025__04__14__648863-53-7-18
    Average 99 stars, based on 1 article reviews
    source software fiji imagej - by Bioz Stars, 2026-09
    99/100 stars
    		  Buy from Supplier
    fiji image j open source software  (Oxford Instruments)
    99
    Oxford Instruments fiji image j open source software
    Fiji Image J Open Source Software, supplied by Oxford Instruments, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/source+software+fiji/Imaris/bio_rxiv__2024__10__27__620431-412-4-11
    Average 99 stars, based on 1 article reviews
    fiji image j open source software - by Bioz Stars, 2026-09
    99/100 stars
    		  Buy from Supplier
    source image processing software imagej fiji v2 14 0  (Oxford Instruments)
    99
    Oxford Instruments source image processing software imagej fiji v2 14 0
    Source Image Processing Software Imagej Fiji V2 14 0, supplied by Oxford Instruments, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/source+software+fiji/Imaris/pmc11263341-267-6-13
    Average 99 stars, based on 1 article reviews
    source image processing software imagej fiji v2 14 0 - by Bioz Stars, 2026-09
    99/100 stars
    		  Buy from Supplier
    source image processing software imagej fiji v2 14 054  (Oxford Instruments)
    99
    Oxford Instruments source image processing software imagej fiji v2 14 054
    Source Image Processing Software Imagej Fiji V2 14 054, supplied by Oxford Instruments, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/source+software+fiji/Imaris/pm39039235-291-6-13
    Average 99 stars, based on 1 article reviews
    source image processing software imagej fiji v2 14 054 - by Bioz Stars, 2026-09
    99/100 stars
    		  Buy from Supplier

    Image Search Results