Virus:Article Title: Infraslow histaminergic dynamics govern priming states to gate moment-to-moment memory accessibility.
Article Snippet: The study adhered to the Hokkaido University and Nagoya City University guidelines for the care and use of laboratory animals and complied with national guidelines, including the Guidelines for Proper Conduct of Animal Experiments (Science Council of Japan), the Fundamental Guidelines for Proper Conduct of Animal Experiments and Related Activities in Academic Research Institutions (Ministry of Education, Culture, Sports, Science and Technology, Notice No. 71 of 2006) and the Standards for Breeding and Housing of and Pain Alleviation for Experimental Animals (Ministry of the Environment, Notice No. 88 of 2006). .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-HDC Progen Biotechnik GmbH Cat. #16045; RRID:AB_2773044 Alexa Fluor 594 donkey anti-rabbit IgG Thermo Fisher Scientific Cat. #A21207; RRID:AB_141637 goat polyclonal anti-GFP Abcam Cat. #AB6673; RRID:AB_305643 peroxidase-conjugated F(ab’)2 donkey anti-goat IgG (H+L) Jackson ImmunoResearch Cat. #705-036-147; RRID:AB_2340392 Bacterial and virus strains AAVdj-CaMKIIα-GCaMP6m UNC Vector Core N/A AAVdj-Ef1α-DIO-GCaMP6s UNC Vector Core N/A AAV5-Ef1α-DIO-eNpHR3.0-mCherry UNC Vector Core N/A AAV5-Ef1α-DIO-mCherry UNC Vector Core N/A AAV5-Ef1α-DIO-eNpHR3.0-EYFP Gradinaru et al.57 Addgene #26966-AAV5 AAV9-Ef1α-DIO-hChR2(H134R)-EYFP Karl Deisseroth, unpublished Addgene #20298-AAV9 AAV9-Ef1α-DIO-EYFP Karl Deisseroth, unpublished Addgene #27056-AAV9 Chemicals, peptides, and recombinant proteins DAPI Dojindo Cat. #D523 CF488A Tyramide Biotium Cat. #92171 Glucose oxidase Sigma-Aldrich Cat. #G7141 β-D-glucose Wako Pure Chemical Industries Cat. #049-31165 Experimental models: Organisms/strains HDC-IRES-Cre Jackson Laboratory #021198; RRID:IMSR_JAX:021198 Software and algorithms GraphPad Prism 10.4.0 GraphPad Software RRID:SCR_002798 Python Python Software Foundation RRID:SCR_008394 MATLAB MathWorks RRID:SCR_001622 pyPhotometry Akam and Walton.58 https://github.com/pyphotometry CaImAn Giovannucci et al.59 https://github.com/flatironinstitute/CaImAn DeepLabCut Mathis et al.60 https://github.com/DeepLabCut ll OPEN ACCESSArticle Neuron 114, 1–14.e1–e10, November 11, 2026 e1 .. The viral vectors AAVdj-CaMKIIα-GCaMP6m (UNC Vector Core (Chapel Hill, North Carolina, USA)), AAVdj-Ef1α-DIO-GCaMP6s (UNC Vector Core), AAV5-Ef1α-DIO-eNpHR3.0-mCherry (UNC Vector Core), AAV5-Ef1α-DIO-mCherry (UNC Vector Core), AAV5-Ef1α-DIO-eNpHR3.0-EYFP57 (Addgene (Watertown, Massachusetts, USA) viral prep #26966-AAV5), AAV9-Ef1α-DIOhChR2(H134R)-EYFP (Addgene viral prep #20298-AAV9), and AAV9-Ef1α-DIO-EYFP (Addgene viral prep #27056-AAV9), kindly provided by Karl Deisseroth, were used in the study.
Article Title: Association learning drives synaptic plasticity at feedforward synapses in somatosensory cortex.
Article Snippet: .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bacterial and virus strains AAV1-hSyn-hChR2(H134R)-eYFP Addgene Cat# 26973-AAV1 AAV9-Ef1a-DIO-hChR2(H134R)-eYFP-WPRE-HGHpA Addgene Cat# 20298-AAV9 pAAV9-EF1a-DIO-hChR2(H134R)-mCherry Addgene Cat# 20297-AAV9 Chemicals, peptides, and recombinant proteins Alexa 568 Invitrogen Cat# A10437 Alexa 488 Invitrogen Cat# A10436 D-AP5 Hellobio Cat# HB0225 Tetrodotoxin citrate Hellobio Cat# HB1035 Picrotoxin Hellobio Cat# HB0506 Lidocain N-ethyl bromide Sigma-Aldrich Cat# L5783 Isoflurane Patterson Veterinary Pivetal Ketoprofen Sigma-Aldrich Cat# K1751 Experimental models: organisms/strains C57BL/6J mice Jackson Laboratory RRID:IMSR_JAX:000664 Scnn1a-tg3-Cre mice Jackson Laboratory RRID:IMSR_JAX:009613 fosGFP (1–3 strain) mice Carnegie Mellon University Nelf-Cre mice MMRRC RRID:MMRRC_037424-UCD Ai32 mice Jackson Laboratory RRID:IMSR_JAX:024109 Software and algorithms Igor Pro 6.37 Wavemetrics https://www.wavemetrics.com/products/igorpro Origin Pro (2022b) OriginLab https://www.originlab.com/ MATLAB Mathworks Inc. https://www.mathworks.com/ Minianalysis 6 Synaptosoft Custom codes for sensory association training Audette et al. 2019 https://github.com/barthlab/Sensory- association- training - behavior Custom code for regression discontinuity tree This paper https://github.com/barthlab/RegressionDiscontinuityTree Other IR beam-break sensor Adafruit Cat# 2167 Yun Shield v2.4 Dragino Discontinued Leonardo Arduino Cat# A000057 Relay shield for Arduino v2.1 DFRobot Cat# DFR0144 Capacitive touch sensor Adafruit Cat# 1374 Solenoid valve The Lee Company Cat# LHDA1233115H Gas regulator Fisherbrand Cat# 10-575-105 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . D ow nloaded from https://academ ic.oup.com /cercor/article/36/6/bhag047/8703142 by guest on 20 June 2026 Experimental model and study participant details Scnn1a-tg3-Cre mice were used to virally express channelrhodopsin2 (ChR2) in excitatory neurons of L4. ..
Recombinant:Article Title: Infraslow histaminergic dynamics govern priming states to gate moment-to-moment memory accessibility.
Article Snippet: The study adhered to the Hokkaido University and Nagoya City University guidelines for the care and use of laboratory animals and complied with national guidelines, including the Guidelines for Proper Conduct of Animal Experiments (Science Council of Japan), the Fundamental Guidelines for Proper Conduct of Animal Experiments and Related Activities in Academic Research Institutions (Ministry of Education, Culture, Sports, Science and Technology, Notice No. 71 of 2006) and the Standards for Breeding and Housing of and Pain Alleviation for Experimental Animals (Ministry of the Environment, Notice No. 88 of 2006). .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-HDC Progen Biotechnik GmbH Cat. #16045; RRID:AB_2773044 Alexa Fluor 594 donkey anti-rabbit IgG Thermo Fisher Scientific Cat. #A21207; RRID:AB_141637 goat polyclonal anti-GFP Abcam Cat. #AB6673; RRID:AB_305643 peroxidase-conjugated F(ab’)2 donkey anti-goat IgG (H+L) Jackson ImmunoResearch Cat. #705-036-147; RRID:AB_2340392 Bacterial and virus strains AAVdj-CaMKIIα-GCaMP6m UNC Vector Core N/A AAVdj-Ef1α-DIO-GCaMP6s UNC Vector Core N/A AAV5-Ef1α-DIO-eNpHR3.0-mCherry UNC Vector Core N/A AAV5-Ef1α-DIO-mCherry UNC Vector Core N/A AAV5-Ef1α-DIO-eNpHR3.0-EYFP Gradinaru et al.57 Addgene #26966-AAV5 AAV9-Ef1α-DIO-hChR2(H134R)-EYFP Karl Deisseroth, unpublished Addgene #20298-AAV9 AAV9-Ef1α-DIO-EYFP Karl Deisseroth, unpublished Addgene #27056-AAV9 Chemicals, peptides, and recombinant proteins DAPI Dojindo Cat. #D523 CF488A Tyramide Biotium Cat. #92171 Glucose oxidase Sigma-Aldrich Cat. #G7141 β-D-glucose Wako Pure Chemical Industries Cat. #049-31165 Experimental models: Organisms/strains HDC-IRES-Cre Jackson Laboratory #021198; RRID:IMSR_JAX:021198 Software and algorithms GraphPad Prism 10.4.0 GraphPad Software RRID:SCR_002798 Python Python Software Foundation RRID:SCR_008394 MATLAB MathWorks RRID:SCR_001622 pyPhotometry Akam and Walton.58 https://github.com/pyphotometry CaImAn Giovannucci et al.59 https://github.com/flatironinstitute/CaImAn DeepLabCut Mathis et al.60 https://github.com/DeepLabCut ll OPEN ACCESSArticle Neuron 114, 1–14.e1–e10, November 11, 2026 e1 .. The viral vectors AAVdj-CaMKIIα-GCaMP6m (UNC Vector Core (Chapel Hill, North Carolina, USA)), AAVdj-Ef1α-DIO-GCaMP6s (UNC Vector Core), AAV5-Ef1α-DIO-eNpHR3.0-mCherry (UNC Vector Core), AAV5-Ef1α-DIO-mCherry (UNC Vector Core), AAV5-Ef1α-DIO-eNpHR3.0-EYFP57 (Addgene (Watertown, Massachusetts, USA) viral prep #26966-AAV5), AAV9-Ef1α-DIOhChR2(H134R)-EYFP (Addgene viral prep #20298-AAV9), and AAV9-Ef1α-DIO-EYFP (Addgene viral prep #27056-AAV9), kindly provided by Karl Deisseroth, were used in the study.
Article Title: Association learning drives synaptic plasticity at feedforward synapses in somatosensory cortex.
Article Snippet: .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bacterial and virus strains AAV1-hSyn-hChR2(H134R)-eYFP Addgene Cat# 26973-AAV1 AAV9-Ef1a-DIO-hChR2(H134R)-eYFP-WPRE-HGHpA Addgene Cat# 20298-AAV9 pAAV9-EF1a-DIO-hChR2(H134R)-mCherry Addgene Cat# 20297-AAV9 Chemicals, peptides, and recombinant proteins Alexa 568 Invitrogen Cat# A10437 Alexa 488 Invitrogen Cat# A10436 D-AP5 Hellobio Cat# HB0225 Tetrodotoxin citrate Hellobio Cat# HB1035 Picrotoxin Hellobio Cat# HB0506 Lidocain N-ethyl bromide Sigma-Aldrich Cat# L5783 Isoflurane Patterson Veterinary Pivetal Ketoprofen Sigma-Aldrich Cat# K1751 Experimental models: organisms/strains C57BL/6J mice Jackson Laboratory RRID:IMSR_JAX:000664 Scnn1a-tg3-Cre mice Jackson Laboratory RRID:IMSR_JAX:009613 fosGFP (1–3 strain) mice Carnegie Mellon University Nelf-Cre mice MMRRC RRID:MMRRC_037424-UCD Ai32 mice Jackson Laboratory RRID:IMSR_JAX:024109 Software and algorithms Igor Pro 6.37 Wavemetrics https://www.wavemetrics.com/products/igorpro Origin Pro (2022b) OriginLab https://www.originlab.com/ MATLAB Mathworks Inc. https://www.mathworks.com/ Minianalysis 6 Synaptosoft Custom codes for sensory association training Audette et al. 2019 https://github.com/barthlab/Sensory- association- training - behavior Custom code for regression discontinuity tree This paper https://github.com/barthlab/RegressionDiscontinuityTree Other IR beam-break sensor Adafruit Cat# 2167 Yun Shield v2.4 Dragino Discontinued Leonardo Arduino Cat# A000057 Relay shield for Arduino v2.1 DFRobot Cat# DFR0144 Capacitive touch sensor Adafruit Cat# 1374 Solenoid valve The Lee Company Cat# LHDA1233115H Gas regulator Fisherbrand Cat# 10-575-105 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . D ow nloaded from https://academ ic.oup.com /cercor/article/36/6/bhag047/8703142 by guest on 20 June 2026 Experimental model and study participant details Scnn1a-tg3-Cre mice were used to virally express channelrhodopsin2 (ChR2) in excitatory neurons of L4. ..
Article Title: A multi-organ metabolomics atlas reveals molecular dysregulations in Alzheimer's disease mouse models.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Mouse - Brain Caltech, Pasadena N/A Mouse - Liver Caltech, Pasadena N/A Mouse - Serum Caltech, Pasadena N/A Mouse - Cecal content Caltech, Pasadena N/A Mouse - Feces Caltech, Pasadena N/A Human - Serum/Plasma Alzheimer Gut Microbiome Project N/A Chemicals, peptides, and recombinant proteins Water, OptimaTM LC/MS Grade Fisher Chemical W6-4 Methanol, OptimaTM LC/MS Grade Fisher Chemical A456-500 L-Carnitine hydrochloride MilliporeSigma 6645-46-1 Phenylpropionyl chloride MilliporeSigma 645-45-4 Phenylacetyl chloride MilliporeSigma 103-80-0 Benzoyl chloride MilliporeSigma 98-88-4 Pyridine MilliporeSigma 110-86-1 Critical commercial assays Phree Phospholipid Removal Phenomenex 8E-S133-TGB MagMAX Microbiome Ultra Total Nucleic Acid Isolation Kit Thermo Fisher Scientific Cat#A42357 Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Scientific Cat#P11496 KAPA HyperPlus Roche Cat#KK8514 NovaSeq 6000 S4 flowcell v1.5 (300-cycle) Illumina Cat#20028312 Deposited data LC-MS/MS - Mouse Brain This paper MassIVE: MSV000096035 LC-MS/MS - Mouse Liver This paper MassIVE: MSV000096037 LC-MS/MS - Mouse Serum This paper MassIVE: MSV000096036 LC-MS/MS - Mouse Cecal Content This paper MassIVE: MSV000096038 LC-MS/MS - GF Mouse Feces This paper MassIVE: MSV000096039 LC-MS/MS - 3xTg Mouse Feces This paper MassIVE: MSV000093230 LC-MS/MS - 5xFAD Mouse Feces This paper MassIVE: MSV000093168 Metagenomics - 3xTg Mouse Feces This paper ENA: ERP165389 Metagenomics - 5xFAD Mouse Feces This paper ENA; ERP165388 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat#000664 Mouse: B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax The Jackson Laboratory Cat#004807 Mouse: B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax The Jackson Laboratory Cat#034848 Software and algorithms R version 4.5.2 The R Foundation https://www.r-project.org/ MZmine version 3.9 mzio https://mzio.io/mzmine-news/ GNPS2 GNPS2 https://gnps2.org/homepage PanReDU El Abiead et al.59 https://redu.gnps2.org/selection/ (Continued on next page) 18 Cell Reports 45, 117499, June 23, 2026 .. As previously described,55 8-weeks-old wild-type C57BL/6J mice (The Jackson Laboratory, Cat#000664), homozygous 3xTg22 [B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax] (The Jackson Laboratory, Cat#004807) and hemizygous 5xFAD23 [B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax] (The Jackson Laboratory, Cat#034848) mice were obtained from the Jackson Laboratory and maintained in the laboratory of S.K.M at the California Institute of Technology (Caltech).
Article Title: Genetic inactivation of Translin/Trax RNase disrupts miRNAs, hippocampal synaptic plasticity, and memory.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins miRVana miRNA Isolation Kit with phenol Thermo Fisher Scientific Cat # AM1560 DNase I Zymo Cat # E1010 Illumina TruSeq Small RNA Library Preparation Kit Illumina Cat # RS-200 Illumina Stranded mRNA Library Preparation Kit Illumina Cat # 20040532 iScript cDNA Synthesis Kit Bio-Rad Cat # 1708890 SYBRTM Green Universal Master Mix Thermo Fisher Cat # 4309155 Deposited data Trax miRNA sequencing data This study [Gene Expression Omnibus (GEO)]: [GSE300964] Trax mRNA sequencing data This study [Gene Expression Omnibus (GEO)]: [GSE300964] Experimental models: Organisms/strains C57BL/6-Tsnax em1Jbar /J Jackson Lab strain # 035903 Oligonucleotides See Table S1 for the qPCR primers Integrated DNA Technology (IDT), Coralville, IA, USA N/A Software and algorithms GraphPad Prism GraphPad N/A BioRender BioRender N/A Adobe Illustrator 2024 Adobe N/A Axon pCLAMP 10 Suite (Clampex and Clampfit) Molecular Devices, CA Axon pCLAMP Partek Flow Partek, Illumina, CA Partek Flow ExpressAnalyst110 Express Analyst ExpressAnalyst Venn Diagram Maker Good Calculators Venn Diagram Maker | Good Calculators STRING111 STRING Consortium 2025 STRING: functional protein association networks Ethovision XT Noldus, Leesburg, VA, USA EthoVision XT | Video tracking software | Noldus BORIS Behavioral Analysis Software Olivier Friard, University of Torino, Italy. .. BORIS miRDB miRNA target prediction and functional annotations miRDB - MicroRNA Target Prediction Database FreezeScan System CleverSys Inc., Reston, VA, USA FreezeScan - CleverSys Inc DAVID Bioinformatics Database NIH, USA DAVID Custom Code for gene expression analysis and visualization Zeru Peterson’s Github page Github-ZP-ABC Allen Brain Cell (ABC) Atlas- Mouse Allen Institute ABC Atlas CNS MicroRNA Profiles Washington University School of Medicine, St. Louis CNS MicroRNA Profiles Other Teklad irradiated S-2335 mouse breeder diet #7904 Inotiv Teklad Diet, Bedding and Enrichment (Continued on next page) iScience 29, 116188, June 19, 2026 e1
Software:Article Title: Infraslow histaminergic dynamics govern priming states to gate moment-to-moment memory accessibility.
Article Snippet: The study adhered to the Hokkaido University and Nagoya City University guidelines for the care and use of laboratory animals and complied with national guidelines, including the Guidelines for Proper Conduct of Animal Experiments (Science Council of Japan), the Fundamental Guidelines for Proper Conduct of Animal Experiments and Related Activities in Academic Research Institutions (Ministry of Education, Culture, Sports, Science and Technology, Notice No. 71 of 2006) and the Standards for Breeding and Housing of and Pain Alleviation for Experimental Animals (Ministry of the Environment, Notice No. 88 of 2006). .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-HDC Progen Biotechnik GmbH Cat. #16045; RRID:AB_2773044 Alexa Fluor 594 donkey anti-rabbit IgG Thermo Fisher Scientific Cat. #A21207; RRID:AB_141637 goat polyclonal anti-GFP Abcam Cat. #AB6673; RRID:AB_305643 peroxidase-conjugated F(ab’)2 donkey anti-goat IgG (H+L) Jackson ImmunoResearch Cat. #705-036-147; RRID:AB_2340392 Bacterial and virus strains AAVdj-CaMKIIα-GCaMP6m UNC Vector Core N/A AAVdj-Ef1α-DIO-GCaMP6s UNC Vector Core N/A AAV5-Ef1α-DIO-eNpHR3.0-mCherry UNC Vector Core N/A AAV5-Ef1α-DIO-mCherry UNC Vector Core N/A AAV5-Ef1α-DIO-eNpHR3.0-EYFP Gradinaru et al.57 Addgene #26966-AAV5 AAV9-Ef1α-DIO-hChR2(H134R)-EYFP Karl Deisseroth, unpublished Addgene #20298-AAV9 AAV9-Ef1α-DIO-EYFP Karl Deisseroth, unpublished Addgene #27056-AAV9 Chemicals, peptides, and recombinant proteins DAPI Dojindo Cat. #D523 CF488A Tyramide Biotium Cat. #92171 Glucose oxidase Sigma-Aldrich Cat. #G7141 β-D-glucose Wako Pure Chemical Industries Cat. #049-31165 Experimental models: Organisms/strains HDC-IRES-Cre Jackson Laboratory #021198; RRID:IMSR_JAX:021198 Software and algorithms GraphPad Prism 10.4.0 GraphPad Software RRID:SCR_002798 Python Python Software Foundation RRID:SCR_008394 MATLAB MathWorks RRID:SCR_001622 pyPhotometry Akam and Walton.58 https://github.com/pyphotometry CaImAn Giovannucci et al.59 https://github.com/flatironinstitute/CaImAn DeepLabCut Mathis et al.60 https://github.com/DeepLabCut ll OPEN ACCESSArticle Neuron 114, 1–14.e1–e10, November 11, 2026 e1 .. The viral vectors AAVdj-CaMKIIα-GCaMP6m (UNC Vector Core (Chapel Hill, North Carolina, USA)), AAVdj-Ef1α-DIO-GCaMP6s (UNC Vector Core), AAV5-Ef1α-DIO-eNpHR3.0-mCherry (UNC Vector Core), AAV5-Ef1α-DIO-mCherry (UNC Vector Core), AAV5-Ef1α-DIO-eNpHR3.0-EYFP57 (Addgene (Watertown, Massachusetts, USA) viral prep #26966-AAV5), AAV9-Ef1α-DIOhChR2(H134R)-EYFP (Addgene viral prep #20298-AAV9), and AAV9-Ef1α-DIO-EYFP (Addgene viral prep #27056-AAV9), kindly provided by Karl Deisseroth, were used in the study.
Article Title: A multi-organ metabolomics atlas reveals molecular dysregulations in Alzheimer's disease mouse models.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Mouse - Brain Caltech, Pasadena N/A Mouse - Liver Caltech, Pasadena N/A Mouse - Serum Caltech, Pasadena N/A Mouse - Cecal content Caltech, Pasadena N/A Mouse - Feces Caltech, Pasadena N/A Human - Serum/Plasma Alzheimer Gut Microbiome Project N/A Chemicals, peptides, and recombinant proteins Water, OptimaTM LC/MS Grade Fisher Chemical W6-4 Methanol, OptimaTM LC/MS Grade Fisher Chemical A456-500 L-Carnitine hydrochloride MilliporeSigma 6645-46-1 Phenylpropionyl chloride MilliporeSigma 645-45-4 Phenylacetyl chloride MilliporeSigma 103-80-0 Benzoyl chloride MilliporeSigma 98-88-4 Pyridine MilliporeSigma 110-86-1 Critical commercial assays Phree Phospholipid Removal Phenomenex 8E-S133-TGB MagMAX Microbiome Ultra Total Nucleic Acid Isolation Kit Thermo Fisher Scientific Cat#A42357 Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Scientific Cat#P11496 KAPA HyperPlus Roche Cat#KK8514 NovaSeq 6000 S4 flowcell v1.5 (300-cycle) Illumina Cat#20028312 Deposited data LC-MS/MS - Mouse Brain This paper MassIVE: MSV000096035 LC-MS/MS - Mouse Liver This paper MassIVE: MSV000096037 LC-MS/MS - Mouse Serum This paper MassIVE: MSV000096036 LC-MS/MS - Mouse Cecal Content This paper MassIVE: MSV000096038 LC-MS/MS - GF Mouse Feces This paper MassIVE: MSV000096039 LC-MS/MS - 3xTg Mouse Feces This paper MassIVE: MSV000093230 LC-MS/MS - 5xFAD Mouse Feces This paper MassIVE: MSV000093168 Metagenomics - 3xTg Mouse Feces This paper ENA: ERP165389 Metagenomics - 5xFAD Mouse Feces This paper ENA; ERP165388 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat#000664 Mouse: B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax The Jackson Laboratory Cat#004807 Mouse: B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax The Jackson Laboratory Cat#034848 Software and algorithms R version 4.5.2 The R Foundation https://www.r-project.org/ MZmine version 3.9 mzio https://mzio.io/mzmine-news/ GNPS2 GNPS2 https://gnps2.org/homepage PanReDU El Abiead et al.59 https://redu.gnps2.org/selection/ (Continued on next page) 18 Cell Reports 45, 117499, June 23, 2026 .. As previously described,55 8-weeks-old wild-type C57BL/6J mice (The Jackson Laboratory, Cat#000664), homozygous 3xTg22 [B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax] (The Jackson Laboratory, Cat#004807) and hemizygous 5xFAD23 [B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax] (The Jackson Laboratory, Cat#034848) mice were obtained from the Jackson Laboratory and maintained in the laboratory of S.K.M at the California Institute of Technology (Caltech).
Article Title: Patient-derived organoids predict personalized drug response and reveal alternative therapeutic options in glioblastoma.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Glioblastoma organoid lines This paper Table S1 Experimental models: Organisms/strains NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ Jackson Laboratory Strain #:005557 RRID:IMSR_JAX:005557 Oligonucleotides Primers, see Table S5 This paper N/A Software and algorithms R software R project for statistical computing https://www.r-project.org/ Prism 8, v8 GraphPad software https://www.graphpad.com/ FASTP (v0.23.2) Chen et al.62 https://www.bioinformatics.babraham.ac. uk/projects/fastqc Burrows-Wheeler Aligner (v0.7.17-r1188) Li et al.63 N/A Samtools(v1.16.1) Li et al.64 N/A Genome Analysis Toolkit (GATK4 v4.2.6.1) Li et al.64 https://gatk.broadinstitute.org/hc.en-us ApplyBQSR Pedersen et al.65 N/A Ensemble Variant Effect Predictor (v106.1) McLaren et al.66 N/A Vcf2maf(v1.6.21) McLaren et al.66 N/A CNVkit(v0.9.9) Talevich et al.67 N/A deconstructSigs (v1.9.0) Rosenthal et al.68 N/A STAR (v2.7.9a) Dobin et al.69 N/A RSEM(v1.3.1) Li et al.70 N/A Gene Set Variation Analysis (GSVA) Subramanial et al.71 N/A Gene Set Enrichment Analysis (GSEA) Hänzelmann et al.72 N/A BioRender – https://www.biorender.com/ The R script used for the NGS data analysis This paper https://github.com/SGMedical/GBO e2 Cell Reports Medicine 7, 102850, July 21, 2026 Article ll OPEN ACCESS The EOR was assessed according to the report from the response assessment in neuro-oncology (RANO) resection group and dichotomized into favorable (supramaximal and maximal contrast-enhancing resection) and unfavorable (submaximal contrastenhancing resection and biopsy) resection.34 The methylation status of the MGMT promoter was retrieved from pathological reports based on the result of methylation-specific polymerase chain reaction (MS-PCR, Seoul Clinical Laboratories). ..
Article Title: Genetic inactivation of Translin/Trax RNase disrupts miRNAs, hippocampal synaptic plasticity, and memory.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins miRVana miRNA Isolation Kit with phenol Thermo Fisher Scientific Cat # AM1560 DNase I Zymo Cat # E1010 Illumina TruSeq Small RNA Library Preparation Kit Illumina Cat # RS-200 Illumina Stranded mRNA Library Preparation Kit Illumina Cat # 20040532 iScript cDNA Synthesis Kit Bio-Rad Cat # 1708890 SYBRTM Green Universal Master Mix Thermo Fisher Cat # 4309155 Deposited data Trax miRNA sequencing data This study [Gene Expression Omnibus (GEO)]: [GSE300964] Trax mRNA sequencing data This study [Gene Expression Omnibus (GEO)]: [GSE300964] Experimental models: Organisms/strains C57BL/6-Tsnax em1Jbar /J Jackson Lab strain # 035903 Oligonucleotides See Table S1 for the qPCR primers Integrated DNA Technology (IDT), Coralville, IA, USA N/A Software and algorithms GraphPad Prism GraphPad N/A BioRender BioRender N/A Adobe Illustrator 2024 Adobe N/A Axon pCLAMP 10 Suite (Clampex and Clampfit) Molecular Devices, CA Axon pCLAMP Partek Flow Partek, Illumina, CA Partek Flow ExpressAnalyst110 Express Analyst ExpressAnalyst Venn Diagram Maker Good Calculators Venn Diagram Maker | Good Calculators STRING111 STRING Consortium 2025 STRING: functional protein association networks Ethovision XT Noldus, Leesburg, VA, USA EthoVision XT | Video tracking software | Noldus BORIS Behavioral Analysis Software Olivier Friard, University of Torino, Italy. .. BORIS miRDB miRNA target prediction and functional annotations miRDB - MicroRNA Target Prediction Database FreezeScan System CleverSys Inc., Reston, VA, USA FreezeScan - CleverSys Inc DAVID Bioinformatics Database NIH, USA DAVID Custom Code for gene expression analysis and visualization Zeru Peterson’s Github page Github-ZP-ABC Allen Brain Cell (ABC) Atlas- Mouse Allen Institute ABC Atlas CNS MicroRNA Profiles Washington University School of Medicine, St. Louis CNS MicroRNA Profiles Other Teklad irradiated S-2335 mouse breeder diet #7904 Inotiv Teklad Diet, Bedding and Enrichment (Continued on next page) iScience 29, 116188, June 19, 2026 e1
other:Article Title: A cell-intrinsic glucocorticoid biosynthesis and sensing circuit maintains a homeostatic Th17 cell state.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Ccr8 (Mm99999115_s1; Mouse) Thermo Fisher Scientific Cat# 4331182 ACTIN (Hs01060665_g1; Human) Thermo Fisher Scientific Cat# 4331182 TSC22D3 (Hs00608272_m1; Human) Thermo Fisher Scientific Cat# 4331182 CYP11A1 (Hs00167984_m1; Human) Thermo Fisher Scientific Cat# 4331182 Deposited data RNA-seq on T cells This paper GEO: GSE296482 ATAC-seq on T cells This paper GEO: GSE320348 Mass spectrometry proteomics data This paper PRIDE: PXD063776 scRNA-seq of in vivo Th17 cells Schnell et al.5 GEO: GSE188320 scRNA-seq of in vitro Th17 cells Gaublomme et al.20 GEO: GSE74833 ATAC-seq on CD4 T cells (Figure 2A) Thakore et al.21 GEO: GSE206607 and GSE296490 ATAC-seq on in vivo Th17 cells (Table S6) Schnell et al.1 GEO: GSE188319 IRF4 ATAC-seq Pham et al.25 GEO: GSE123206 IRF4 ChIP-seq Pham et al.25 GEO: GSE123198 STAT3 ATAC-seq Chang et al.50 GEO: GSE153442 pSTAT3 ChIP-seq Durant et al.51 GEO: GSE21669 SMAD4 ChIP-seq Zhang et al.52 GEO: GSE101593 Experimental models: Cell lines PlatE Cell Biolabs, Inc. Cat# RV-101 Experimental models: Organisms/strains C57BL/6J Jackson laboratory Strain ID 000664 C57BL/6-Tg(Tcra2D2,Tcrb2D2)1Kuch/J Jackson laboratory Strain ID 006912 B6.Cg-Tg(Cd4-cre)1Cwi/BfluJ Jackson laboratory Strain ID 022071 B6.Cg-Tg(Lck-icre)3779Nik/J Jackson laboratory Strain ID 012837 C57BL/6-Il17atm1Bcgen/J Jackson laboratory Strain ID 018472 B6.129S7-Rag1tm1Mom/J Jackson laboratory Strain ID 002216 B6(C)-Gt(ROSA)26Sorem1.1 (CAG-cas9*,-EGFP)Rsky/J Jackson laboratory Strain ID 028555 Nr3c1fl/fl Jackson laboratory Strain ID 021021 Cyp11a1fl/fl Acharya et al.12 N/A Fosl2fl/fl Zhang et al.53 N/A Stat3fl/fl Zhang et al.53 N/A Recombinant DNA MSCV-gRNA-Jun This paper N/A MSCV-gRNA-Irf4 This paper N/A MSCV-gRNA-Smad2 This paper N/A MSCV-gRNA-Smad3 This paper N/A MSCV-gRNA-Smad4 This paper N/A MSCV-Jun (OE) This paper N/A MSCV-Fosl2 (OE) This paper N/A MSCV-Irf4 (OE) This paper N/A MSCV-Smad2 (OE) This paper N/A MSCV-Smad3 (OE) This paper N/A MSCV-Smad4 (OE) This paper N/A MSCV-Stat3 (OE) This paper N/A Software and algorithms FlowJo software Tree Star https://flowjo.com Prism 10 GraphPad Software, Inc https://www.graphpad.com/ Code for analyses This paper https://doi.org/10.5281/zenodo.19583152 (Continued on next page) ll OPEN ACCESS Article e4 Immunity 59, 1–18.e1–e10, August 11, 2026
Isolation:Article Title: A multi-organ metabolomics atlas reveals molecular dysregulations in Alzheimer's disease mouse models.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Mouse - Brain Caltech, Pasadena N/A Mouse - Liver Caltech, Pasadena N/A Mouse - Serum Caltech, Pasadena N/A Mouse - Cecal content Caltech, Pasadena N/A Mouse - Feces Caltech, Pasadena N/A Human - Serum/Plasma Alzheimer Gut Microbiome Project N/A Chemicals, peptides, and recombinant proteins Water, OptimaTM LC/MS Grade Fisher Chemical W6-4 Methanol, OptimaTM LC/MS Grade Fisher Chemical A456-500 L-Carnitine hydrochloride MilliporeSigma 6645-46-1 Phenylpropionyl chloride MilliporeSigma 645-45-4 Phenylacetyl chloride MilliporeSigma 103-80-0 Benzoyl chloride MilliporeSigma 98-88-4 Pyridine MilliporeSigma 110-86-1 Critical commercial assays Phree Phospholipid Removal Phenomenex 8E-S133-TGB MagMAX Microbiome Ultra Total Nucleic Acid Isolation Kit Thermo Fisher Scientific Cat#A42357 Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Scientific Cat#P11496 KAPA HyperPlus Roche Cat#KK8514 NovaSeq 6000 S4 flowcell v1.5 (300-cycle) Illumina Cat#20028312 Deposited data LC-MS/MS - Mouse Brain This paper MassIVE: MSV000096035 LC-MS/MS - Mouse Liver This paper MassIVE: MSV000096037 LC-MS/MS - Mouse Serum This paper MassIVE: MSV000096036 LC-MS/MS - Mouse Cecal Content This paper MassIVE: MSV000096038 LC-MS/MS - GF Mouse Feces This paper MassIVE: MSV000096039 LC-MS/MS - 3xTg Mouse Feces This paper MassIVE: MSV000093230 LC-MS/MS - 5xFAD Mouse Feces This paper MassIVE: MSV000093168 Metagenomics - 3xTg Mouse Feces This paper ENA: ERP165389 Metagenomics - 5xFAD Mouse Feces This paper ENA; ERP165388 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat#000664 Mouse: B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax The Jackson Laboratory Cat#004807 Mouse: B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax The Jackson Laboratory Cat#034848 Software and algorithms R version 4.5.2 The R Foundation https://www.r-project.org/ MZmine version 3.9 mzio https://mzio.io/mzmine-news/ GNPS2 GNPS2 https://gnps2.org/homepage PanReDU El Abiead et al.59 https://redu.gnps2.org/selection/ (Continued on next page) 18 Cell Reports 45, 117499, June 23, 2026 .. As previously described,55 8-weeks-old wild-type C57BL/6J mice (The Jackson Laboratory, Cat#000664), homozygous 3xTg22 [B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax] (The Jackson Laboratory, Cat#004807) and hemizygous 5xFAD23 [B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax] (The Jackson Laboratory, Cat#034848) mice were obtained from the Jackson Laboratory and maintained in the laboratory of S.K.M at the California Institute of Technology (Caltech).
Article Title: Genetic inactivation of Translin/Trax RNase disrupts miRNAs, hippocampal synaptic plasticity, and memory.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins miRVana miRNA Isolation Kit with phenol Thermo Fisher Scientific Cat # AM1560 DNase I Zymo Cat # E1010 Illumina TruSeq Small RNA Library Preparation Kit Illumina Cat # RS-200 Illumina Stranded mRNA Library Preparation Kit Illumina Cat # 20040532 iScript cDNA Synthesis Kit Bio-Rad Cat # 1708890 SYBRTM Green Universal Master Mix Thermo Fisher Cat # 4309155 Deposited data Trax miRNA sequencing data This study [Gene Expression Omnibus (GEO)]: [GSE300964] Trax mRNA sequencing data This study [Gene Expression Omnibus (GEO)]: [GSE300964] Experimental models: Organisms/strains C57BL/6-Tsnax em1Jbar /J Jackson Lab strain # 035903 Oligonucleotides See Table S1 for the qPCR primers Integrated DNA Technology (IDT), Coralville, IA, USA N/A Software and algorithms GraphPad Prism GraphPad N/A BioRender BioRender N/A Adobe Illustrator 2024 Adobe N/A Axon pCLAMP 10 Suite (Clampex and Clampfit) Molecular Devices, CA Axon pCLAMP Partek Flow Partek, Illumina, CA Partek Flow ExpressAnalyst110 Express Analyst ExpressAnalyst Venn Diagram Maker Good Calculators Venn Diagram Maker | Good Calculators STRING111 STRING Consortium 2025 STRING: functional protein association networks Ethovision XT Noldus, Leesburg, VA, USA EthoVision XT | Video tracking software | Noldus BORIS Behavioral Analysis Software Olivier Friard, University of Torino, Italy. .. BORIS miRDB miRNA target prediction and functional annotations miRDB - MicroRNA Target Prediction Database FreezeScan System CleverSys Inc., Reston, VA, USA FreezeScan - CleverSys Inc DAVID Bioinformatics Database NIH, USA DAVID Custom Code for gene expression analysis and visualization Zeru Peterson’s Github page Github-ZP-ABC Allen Brain Cell (ABC) Atlas- Mouse Allen Institute ABC Atlas CNS MicroRNA Profiles Washington University School of Medicine, St. Louis CNS MicroRNA Profiles Other Teklad irradiated S-2335 mouse breeder diet #7904 Inotiv Teklad Diet, Bedding and Enrichment (Continued on next page) iScience 29, 116188, June 19, 2026 e1
Picogreen Assay:Article Title: A multi-organ metabolomics atlas reveals molecular dysregulations in Alzheimer's disease mouse models.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Mouse - Brain Caltech, Pasadena N/A Mouse - Liver Caltech, Pasadena N/A Mouse - Serum Caltech, Pasadena N/A Mouse - Cecal content Caltech, Pasadena N/A Mouse - Feces Caltech, Pasadena N/A Human - Serum/Plasma Alzheimer Gut Microbiome Project N/A Chemicals, peptides, and recombinant proteins Water, OptimaTM LC/MS Grade Fisher Chemical W6-4 Methanol, OptimaTM LC/MS Grade Fisher Chemical A456-500 L-Carnitine hydrochloride MilliporeSigma 6645-46-1 Phenylpropionyl chloride MilliporeSigma 645-45-4 Phenylacetyl chloride MilliporeSigma 103-80-0 Benzoyl chloride MilliporeSigma 98-88-4 Pyridine MilliporeSigma 110-86-1 Critical commercial assays Phree Phospholipid Removal Phenomenex 8E-S133-TGB MagMAX Microbiome Ultra Total Nucleic Acid Isolation Kit Thermo Fisher Scientific Cat#A42357 Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Scientific Cat#P11496 KAPA HyperPlus Roche Cat#KK8514 NovaSeq 6000 S4 flowcell v1.5 (300-cycle) Illumina Cat#20028312 Deposited data LC-MS/MS - Mouse Brain This paper MassIVE: MSV000096035 LC-MS/MS - Mouse Liver This paper MassIVE: MSV000096037 LC-MS/MS - Mouse Serum This paper MassIVE: MSV000096036 LC-MS/MS - Mouse Cecal Content This paper MassIVE: MSV000096038 LC-MS/MS - GF Mouse Feces This paper MassIVE: MSV000096039 LC-MS/MS - 3xTg Mouse Feces This paper MassIVE: MSV000093230 LC-MS/MS - 5xFAD Mouse Feces This paper MassIVE: MSV000093168 Metagenomics - 3xTg Mouse Feces This paper ENA: ERP165389 Metagenomics - 5xFAD Mouse Feces This paper ENA; ERP165388 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat#000664 Mouse: B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax The Jackson Laboratory Cat#004807 Mouse: B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax The Jackson Laboratory Cat#034848 Software and algorithms R version 4.5.2 The R Foundation https://www.r-project.org/ MZmine version 3.9 mzio https://mzio.io/mzmine-news/ GNPS2 GNPS2 https://gnps2.org/homepage PanReDU El Abiead et al.59 https://redu.gnps2.org/selection/ (Continued on next page) 18 Cell Reports 45, 117499, June 23, 2026 .. As previously described,55 8-weeks-old wild-type C57BL/6J mice (The Jackson Laboratory, Cat#000664), homozygous 3xTg22 [B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax] (The Jackson Laboratory, Cat#004807) and hemizygous 5xFAD23 [B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax] (The Jackson Laboratory, Cat#034848) mice were obtained from the Jackson Laboratory and maintained in the laboratory of S.K.M at the California Institute of Technology (Caltech).
Metagenomics:Article Title: A multi-organ metabolomics atlas reveals molecular dysregulations in Alzheimer's disease mouse models.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Mouse - Brain Caltech, Pasadena N/A Mouse - Liver Caltech, Pasadena N/A Mouse - Serum Caltech, Pasadena N/A Mouse - Cecal content Caltech, Pasadena N/A Mouse - Feces Caltech, Pasadena N/A Human - Serum/Plasma Alzheimer Gut Microbiome Project N/A Chemicals, peptides, and recombinant proteins Water, OptimaTM LC/MS Grade Fisher Chemical W6-4 Methanol, OptimaTM LC/MS Grade Fisher Chemical A456-500 L-Carnitine hydrochloride MilliporeSigma 6645-46-1 Phenylpropionyl chloride MilliporeSigma 645-45-4 Phenylacetyl chloride MilliporeSigma 103-80-0 Benzoyl chloride MilliporeSigma 98-88-4 Pyridine MilliporeSigma 110-86-1 Critical commercial assays Phree Phospholipid Removal Phenomenex 8E-S133-TGB MagMAX Microbiome Ultra Total Nucleic Acid Isolation Kit Thermo Fisher Scientific Cat#A42357 Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Scientific Cat#P11496 KAPA HyperPlus Roche Cat#KK8514 NovaSeq 6000 S4 flowcell v1.5 (300-cycle) Illumina Cat#20028312 Deposited data LC-MS/MS - Mouse Brain This paper MassIVE: MSV000096035 LC-MS/MS - Mouse Liver This paper MassIVE: MSV000096037 LC-MS/MS - Mouse Serum This paper MassIVE: MSV000096036 LC-MS/MS - Mouse Cecal Content This paper MassIVE: MSV000096038 LC-MS/MS - GF Mouse Feces This paper MassIVE: MSV000096039 LC-MS/MS - 3xTg Mouse Feces This paper MassIVE: MSV000093230 LC-MS/MS - 5xFAD Mouse Feces This paper MassIVE: MSV000093168 Metagenomics - 3xTg Mouse Feces This paper ENA: ERP165389 Metagenomics - 5xFAD Mouse Feces This paper ENA; ERP165388 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat#000664 Mouse: B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax The Jackson Laboratory Cat#004807 Mouse: B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax The Jackson Laboratory Cat#034848 Software and algorithms R version 4.5.2 The R Foundation https://www.r-project.org/ MZmine version 3.9 mzio https://mzio.io/mzmine-news/ GNPS2 GNPS2 https://gnps2.org/homepage PanReDU El Abiead et al.59 https://redu.gnps2.org/selection/ (Continued on next page) 18 Cell Reports 45, 117499, June 23, 2026 .. As previously described,55 8-weeks-old wild-type C57BL/6J mice (The Jackson Laboratory, Cat#000664), homozygous 3xTg22 [B6;129-Tg(APPSwe, tauP301L)1Lfa Psen1tm1Mpm/Mmjax] (The Jackson Laboratory, Cat#004807) and hemizygous 5xFAD23 [B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax] (The Jackson Laboratory, Cat#034848) mice were obtained from the Jackson Laboratory and maintained in the laboratory of S.K.M at the California Institute of Technology (Caltech).
Variant Assay:Article Title: Patient-derived organoids predict personalized drug response and reveal alternative therapeutic options in glioblastoma.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Glioblastoma organoid lines This paper Table S1 Experimental models: Organisms/strains NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ Jackson Laboratory Strain #:005557 RRID:IMSR_JAX:005557 Oligonucleotides Primers, see Table S5 This paper N/A Software and algorithms R software R project for statistical computing https://www.r-project.org/ Prism 8, v8 GraphPad software https://www.graphpad.com/ FASTP (v0.23.2) Chen et al.62 https://www.bioinformatics.babraham.ac. uk/projects/fastqc Burrows-Wheeler Aligner (v0.7.17-r1188) Li et al.63 N/A Samtools(v1.16.1) Li et al.64 N/A Genome Analysis Toolkit (GATK4 v4.2.6.1) Li et al.64 https://gatk.broadinstitute.org/hc.en-us ApplyBQSR Pedersen et al.65 N/A Ensemble Variant Effect Predictor (v106.1) McLaren et al.66 N/A Vcf2maf(v1.6.21) McLaren et al.66 N/A CNVkit(v0.9.9) Talevich et al.67 N/A deconstructSigs (v1.9.0) Rosenthal et al.68 N/A STAR (v2.7.9a) Dobin et al.69 N/A RSEM(v1.3.1) Li et al.70 N/A Gene Set Variation Analysis (GSVA) Subramanial et al.71 N/A Gene Set Enrichment Analysis (GSEA) Hänzelmann et al.72 N/A BioRender – https://www.biorender.com/ The R script used for the NGS data analysis This paper https://github.com/SGMedical/GBO e2 Cell Reports Medicine 7, 102850, July 21, 2026 Article ll OPEN ACCESS The EOR was assessed according to the report from the response assessment in neuro-oncology (RANO) resection group and dichotomized into favorable (supramaximal and maximal contrast-enhancing resection) and unfavorable (submaximal contrastenhancing resection and biopsy) resection.34 The methylation status of the MGMT promoter was retrieved from pathological reports based on the result of methylation-specific polymerase chain reaction (MS-PCR, Seoul Clinical Laboratories). ..
Next-Generation Sequencing:Article Title: Patient-derived organoids predict personalized drug response and reveal alternative therapeutic options in glioblastoma.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Glioblastoma organoid lines This paper Table S1 Experimental models: Organisms/strains NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ Jackson Laboratory Strain #:005557 RRID:IMSR_JAX:005557 Oligonucleotides Primers, see Table S5 This paper N/A Software and algorithms R software R project for statistical computing https://www.r-project.org/ Prism 8, v8 GraphPad software https://www.graphpad.com/ FASTP (v0.23.2) Chen et al.62 https://www.bioinformatics.babraham.ac. uk/projects/fastqc Burrows-Wheeler Aligner (v0.7.17-r1188) Li et al.63 N/A Samtools(v1.16.1) Li et al.64 N/A Genome Analysis Toolkit (GATK4 v4.2.6.1) Li et al.64 https://gatk.broadinstitute.org/hc.en-us ApplyBQSR Pedersen et al.65 N/A Ensemble Variant Effect Predictor (v106.1) McLaren et al.66 N/A Vcf2maf(v1.6.21) McLaren et al.66 N/A CNVkit(v0.9.9) Talevich et al.67 N/A deconstructSigs (v1.9.0) Rosenthal et al.68 N/A STAR (v2.7.9a) Dobin et al.69 N/A RSEM(v1.3.1) Li et al.70 N/A Gene Set Variation Analysis (GSVA) Subramanial et al.71 N/A Gene Set Enrichment Analysis (GSEA) Hänzelmann et al.72 N/A BioRender – https://www.biorender.com/ The R script used for the NGS data analysis This paper https://github.com/SGMedical/GBO e2 Cell Reports Medicine 7, 102850, July 21, 2026 Article ll OPEN ACCESS The EOR was assessed according to the report from the response assessment in neuro-oncology (RANO) resection group and dichotomized into favorable (supramaximal and maximal contrast-enhancing resection) and unfavorable (submaximal contrastenhancing resection and biopsy) resection.34 The methylation status of the MGMT promoter was retrieved from pathological reports based on the result of methylation-specific polymerase chain reaction (MS-PCR, Seoul Clinical Laboratories). ..
Methylation:Article Title: Patient-derived organoids predict personalized drug response and reveal alternative therapeutic options in glioblastoma.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Glioblastoma organoid lines This paper Table S1 Experimental models: Organisms/strains NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ Jackson Laboratory Strain #:005557 RRID:IMSR_JAX:005557 Oligonucleotides Primers, see Table S5 This paper N/A Software and algorithms R software R project for statistical computing https://www.r-project.org/ Prism 8, v8 GraphPad software https://www.graphpad.com/ FASTP (v0.23.2) Chen et al.62 https://www.bioinformatics.babraham.ac. uk/projects/fastqc Burrows-Wheeler Aligner (v0.7.17-r1188) Li et al.63 N/A Samtools(v1.16.1) Li et al.64 N/A Genome Analysis Toolkit (GATK4 v4.2.6.1) Li et al.64 https://gatk.broadinstitute.org/hc.en-us ApplyBQSR Pedersen et al.65 N/A Ensemble Variant Effect Predictor (v106.1) McLaren et al.66 N/A Vcf2maf(v1.6.21) McLaren et al.66 N/A CNVkit(v0.9.9) Talevich et al.67 N/A deconstructSigs (v1.9.0) Rosenthal et al.68 N/A STAR (v2.7.9a) Dobin et al.69 N/A RSEM(v1.3.1) Li et al.70 N/A Gene Set Variation Analysis (GSVA) Subramanial et al.71 N/A Gene Set Enrichment Analysis (GSEA) Hänzelmann et al.72 N/A BioRender – https://www.biorender.com/ The R script used for the NGS data analysis This paper https://github.com/SGMedical/GBO e2 Cell Reports Medicine 7, 102850, July 21, 2026 Article ll OPEN ACCESS The EOR was assessed according to the report from the response assessment in neuro-oncology (RANO) resection group and dichotomized into favorable (supramaximal and maximal contrast-enhancing resection) and unfavorable (submaximal contrastenhancing resection and biopsy) resection.34 The methylation status of the MGMT promoter was retrieved from pathological reports based on the result of methylation-specific polymerase chain reaction (MS-PCR, Seoul Clinical Laboratories). ..
Polymerase Chain Reaction:Article Title: Patient-derived organoids predict personalized drug response and reveal alternative therapeutic options in glioblastoma.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Cell lines Glioblastoma organoid lines This paper Table S1 Experimental models: Organisms/strains NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ Jackson Laboratory Strain #:005557 RRID:IMSR_JAX:005557 Oligonucleotides Primers, see Table S5 This paper N/A Software and algorithms R software R project for statistical computing https://www.r-project.org/ Prism 8, v8 GraphPad software https://www.graphpad.com/ FASTP (v0.23.2) Chen et al.62 https://www.bioinformatics.babraham.ac. uk/projects/fastqc Burrows-Wheeler Aligner (v0.7.17-r1188) Li et al.63 N/A Samtools(v1.16.1) Li et al.64 N/A Genome Analysis Toolkit (GATK4 v4.2.6.1) Li et al.64 https://gatk.broadinstitute.org/hc.en-us ApplyBQSR Pedersen et al.65 N/A Ensemble Variant Effect Predictor (v106.1) McLaren et al.66 N/A Vcf2maf(v1.6.21) McLaren et al.66 N/A CNVkit(v0.9.9) Talevich et al.67 N/A deconstructSigs (v1.9.0) Rosenthal et al.68 N/A STAR (v2.7.9a) Dobin et al.69 N/A RSEM(v1.3.1) Li et al.70 N/A Gene Set Variation Analysis (GSVA) Subramanial et al.71 N/A Gene Set Enrichment Analysis (GSEA) Hänzelmann et al.72 N/A BioRender – https://www.biorender.com/ The R script used for the NGS data analysis This paper https://github.com/SGMedical/GBO e2 Cell Reports Medicine 7, 102850, July 21, 2026 Article ll OPEN ACCESS The EOR was assessed according to the report from the response assessment in neuro-oncology (RANO) resection group and dichotomized into favorable (supramaximal and maximal contrast-enhancing resection) and unfavorable (submaximal contrastenhancing resection and biopsy) resection.34 The methylation status of the MGMT promoter was retrieved from pathological reports based on the result of methylation-specific polymerase chain reaction (MS-PCR, Seoul Clinical Laboratories). ..
Derivative Assay:
Mouse Assay:
CRISPR:
RNA Library Preparation:Article Title: Genetic inactivation of Translin/Trax RNase disrupts miRNAs, hippocampal synaptic plasticity, and memory.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins miRVana miRNA Isolation Kit with phenol Thermo Fisher Scientific Cat # AM1560 DNase I Zymo Cat # E1010 Illumina TruSeq Small RNA Library Preparation Kit Illumina Cat # RS-200 Illumina Stranded mRNA Library Preparation Kit Illumina Cat # 20040532 iScript cDNA Synthesis Kit Bio-Rad Cat # 1708890 SYBRTM Green Universal Master Mix Thermo Fisher Cat # 4309155 Deposited data Trax miRNA sequencing data This study [Gene Expression Omnibus (GEO)]: [GSE300964] Trax mRNA sequencing data This study [Gene Expression Omnibus (GEO)]: [GSE300964] Experimental models: Organisms/strains C57BL/6-Tsnax em1Jbar /J Jackson Lab strain # 035903 Oligonucleotides See Table S1 for the qPCR primers Integrated DNA Technology (IDT), Coralville, IA, USA N/A Software and algorithms GraphPad Prism GraphPad N/A BioRender BioRender N/A Adobe Illustrator 2024 Adobe N/A Axon pCLAMP 10 Suite (Clampex and Clampfit) Molecular Devices, CA Axon pCLAMP Partek Flow Partek, Illumina, CA Partek Flow ExpressAnalyst110 Express Analyst ExpressAnalyst Venn Diagram Maker Good Calculators Venn Diagram Maker | Good Calculators STRING111 STRING Consortium 2025 STRING: functional protein association networks Ethovision XT Noldus, Leesburg, VA, USA EthoVision XT | Video tracking software | Noldus BORIS Behavioral Analysis Software Olivier Friard, University of Torino, Italy. .. BORIS miRDB miRNA target prediction and functional annotations miRDB - MicroRNA Target Prediction Database FreezeScan System CleverSys Inc., Reston, VA, USA FreezeScan - CleverSys Inc DAVID Bioinformatics Database NIH, USA DAVID Custom Code for gene expression analysis and visualization Zeru Peterson’s Github page Github-ZP-ABC Allen Brain Cell (ABC) Atlas- Mouse Allen Institute ABC Atlas CNS MicroRNA Profiles Washington University School of Medicine, St. Louis CNS MicroRNA Profiles Other Teklad irradiated S-2335 mouse breeder diet #7904 Inotiv Teklad Diet, Bedding and Enrichment (Continued on next page) iScience 29, 116188, June 19, 2026 e1
cDNA Synthesis:Article Title: Genetic inactivation of Translin/Trax RNase disrupts miRNAs, hippocampal synaptic plasticity, and memory.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins miRVana miRNA Isolation Kit with phenol Thermo Fisher Scientific Cat # AM1560 DNase I Zymo Cat # E1010 Illumina TruSeq Small RNA Library Preparation Kit Illumina Cat # RS-200 Illumina Stranded mRNA Library Preparation Kit Illumina Cat # 20040532 iScript cDNA Synthesis Kit Bio-Rad Cat # 1708890 SYBRTM Green Universal Master Mix Thermo Fisher Cat # 4309155 Deposited data Trax miRNA sequencing data This study [Gene Expression Omnibus (GEO)]: [GSE300964] Trax mRNA sequencing data This study [Gene Expression Omnibus (GEO)]: [GSE300964] Experimental models: Organisms/strains C57BL/6-Tsnax em1Jbar /J Jackson Lab strain # 035903 Oligonucleotides See Table S1 for the qPCR primers Integrated DNA Technology (IDT), Coralville, IA, USA N/A Software and algorithms GraphPad Prism GraphPad N/A BioRender BioRender N/A Adobe Illustrator 2024 Adobe N/A Axon pCLAMP 10 Suite (Clampex and Clampfit) Molecular Devices, CA Axon pCLAMP Partek Flow Partek, Illumina, CA Partek Flow ExpressAnalyst110 Express Analyst ExpressAnalyst Venn Diagram Maker Good Calculators Venn Diagram Maker | Good Calculators STRING111 STRING Consortium 2025 STRING: functional protein association networks Ethovision XT Noldus, Leesburg, VA, USA EthoVision XT | Video tracking software | Noldus BORIS Behavioral Analysis Software Olivier Friard, University of Torino, Italy. .. BORIS miRDB miRNA target prediction and functional annotations miRDB - MicroRNA Target Prediction Database FreezeScan System CleverSys Inc., Reston, VA, USA FreezeScan - CleverSys Inc DAVID Bioinformatics Database NIH, USA DAVID Custom Code for gene expression analysis and visualization Zeru Peterson’s Github page Github-ZP-ABC Allen Brain Cell (ABC) Atlas- Mouse Allen Institute ABC Atlas CNS MicroRNA Profiles Washington University School of Medicine, St. Louis CNS MicroRNA Profiles Other Teklad irradiated S-2335 mouse breeder diet #7904 Inotiv Teklad Diet, Bedding and Enrichment (Continued on next page) iScience 29, 116188, June 19, 2026 e1
Sequencing:Article Title: Genetic inactivation of Translin/Trax RNase disrupts miRNAs, hippocampal synaptic plasticity, and memory.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins miRVana miRNA Isolation Kit with phenol Thermo Fisher Scientific Cat # AM1560 DNase I Zymo Cat # E1010 Illumina TruSeq Small RNA Library Preparation Kit Illumina Cat # RS-200 Illumina Stranded mRNA Library Preparation Kit Illumina Cat # 20040532 iScript cDNA Synthesis Kit Bio-Rad Cat # 1708890 SYBRTM Green Universal Master Mix Thermo Fisher Cat # 4309155 Deposited data Trax miRNA sequencing data This study [Gene Expression Omnibus (GEO)]: [GSE300964] Trax mRNA sequencing data This study [Gene Expression Omnibus (GEO)]: [GSE300964] Experimental models: Organisms/strains C57BL/6-Tsnax em1Jbar /J Jackson Lab strain # 035903 Oligonucleotides See Table S1 for the qPCR primers Integrated DNA Technology (IDT), Coralville, IA, USA N/A Software and algorithms GraphPad Prism GraphPad N/A BioRender BioRender N/A Adobe Illustrator 2024 Adobe N/A Axon pCLAMP 10 Suite (Clampex and Clampfit) Molecular Devices, CA Axon pCLAMP Partek Flow Partek, Illumina, CA Partek Flow ExpressAnalyst110 Express Analyst ExpressAnalyst Venn Diagram Maker Good Calculators Venn Diagram Maker | Good Calculators STRING111 STRING Consortium 2025 STRING: functional protein association networks Ethovision XT Noldus, Leesburg, VA, USA EthoVision XT | Video tracking software | Noldus BORIS Behavioral Analysis Software Olivier Friard, University of Torino, Italy. .. BORIS miRDB miRNA target prediction and functional annotations miRDB - MicroRNA Target Prediction Database FreezeScan System CleverSys Inc., Reston, VA, USA FreezeScan - CleverSys Inc DAVID Bioinformatics Database NIH, USA DAVID Custom Code for gene expression analysis and visualization Zeru Peterson’s Github page Github-ZP-ABC Allen Brain Cell (ABC) Atlas- Mouse Allen Institute ABC Atlas CNS MicroRNA Profiles Washington University School of Medicine, St. Louis CNS MicroRNA Profiles Other Teklad irradiated S-2335 mouse breeder diet #7904 Inotiv Teklad Diet, Bedding and Enrichment (Continued on next page) iScience 29, 116188, June 19, 2026 e1
Gene Expression:Article Title: Genetic inactivation of Translin/Trax RNase disrupts miRNAs, hippocampal synaptic plasticity, and memory.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins miRVana miRNA Isolation Kit with phenol Thermo Fisher Scientific Cat # AM1560 DNase I Zymo Cat # E1010 Illumina TruSeq Small RNA Library Preparation Kit Illumina Cat # RS-200 Illumina Stranded mRNA Library Preparation Kit Illumina Cat # 20040532 iScript cDNA Synthesis Kit Bio-Rad Cat # 1708890 SYBRTM Green Universal Master Mix Thermo Fisher Cat # 4309155 Deposited data Trax miRNA sequencing data This study [Gene Expression Omnibus (GEO)]: [GSE300964] Trax mRNA sequencing data This study [Gene Expression Omnibus (GEO)]: [GSE300964] Experimental models: Organisms/strains C57BL/6-Tsnax em1Jbar /J Jackson Lab strain # 035903 Oligonucleotides See Table S1 for the qPCR primers Integrated DNA Technology (IDT), Coralville, IA, USA N/A Software and algorithms GraphPad Prism GraphPad N/A BioRender BioRender N/A Adobe Illustrator 2024 Adobe N/A Axon pCLAMP 10 Suite (Clampex and Clampfit) Molecular Devices, CA Axon pCLAMP Partek Flow Partek, Illumina, CA Partek Flow ExpressAnalyst110 Express Analyst ExpressAnalyst Venn Diagram Maker Good Calculators Venn Diagram Maker | Good Calculators STRING111 STRING Consortium 2025 STRING: functional protein association networks Ethovision XT Noldus, Leesburg, VA, USA EthoVision XT | Video tracking software | Noldus BORIS Behavioral Analysis Software Olivier Friard, University of Torino, Italy. .. BORIS miRDB miRNA target prediction and functional annotations miRDB - MicroRNA Target Prediction Database FreezeScan System CleverSys Inc., Reston, VA, USA FreezeScan - CleverSys Inc DAVID Bioinformatics Database NIH, USA DAVID Custom Code for gene expression analysis and visualization Zeru Peterson’s Github page Github-ZP-ABC Allen Brain Cell (ABC) Atlas- Mouse Allen Institute ABC Atlas CNS MicroRNA Profiles Washington University School of Medicine, St. Louis CNS MicroRNA Profiles Other Teklad irradiated S-2335 mouse breeder diet #7904 Inotiv Teklad Diet, Bedding and Enrichment (Continued on next page) iScience 29, 116188, June 19, 2026 e1
Real-time Polymerase Chain Reaction:Article Title: Genetic inactivation of Translin/Trax RNase disrupts miRNAs, hippocampal synaptic plasticity, and memory.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins miRVana miRNA Isolation Kit with phenol Thermo Fisher Scientific Cat # AM1560 DNase I Zymo Cat # E1010 Illumina TruSeq Small RNA Library Preparation Kit Illumina Cat # RS-200 Illumina Stranded mRNA Library Preparation Kit Illumina Cat # 20040532 iScript cDNA Synthesis Kit Bio-Rad Cat # 1708890 SYBRTM Green Universal Master Mix Thermo Fisher Cat # 4309155 Deposited data Trax miRNA sequencing data This study [Gene Expression Omnibus (GEO)]: [GSE300964] Trax mRNA sequencing data This study [Gene Expression Omnibus (GEO)]: [GSE300964] Experimental models: Organisms/strains C57BL/6-Tsnax em1Jbar /J Jackson Lab strain # 035903 Oligonucleotides See Table S1 for the qPCR primers Integrated DNA Technology (IDT), Coralville, IA, USA N/A Software and algorithms GraphPad Prism GraphPad N/A BioRender BioRender N/A Adobe Illustrator 2024 Adobe N/A Axon pCLAMP 10 Suite (Clampex and Clampfit) Molecular Devices, CA Axon pCLAMP Partek Flow Partek, Illumina, CA Partek Flow ExpressAnalyst110 Express Analyst ExpressAnalyst Venn Diagram Maker Good Calculators Venn Diagram Maker | Good Calculators STRING111 STRING Consortium 2025 STRING: functional protein association networks Ethovision XT Noldus, Leesburg, VA, USA EthoVision XT | Video tracking software | Noldus BORIS Behavioral Analysis Software Olivier Friard, University of Torino, Italy. .. BORIS miRDB miRNA target prediction and functional annotations miRDB - MicroRNA Target Prediction Database FreezeScan System CleverSys Inc., Reston, VA, USA FreezeScan - CleverSys Inc DAVID Bioinformatics Database NIH, USA DAVID Custom Code for gene expression analysis and visualization Zeru Peterson’s Github page Github-ZP-ABC Allen Brain Cell (ABC) Atlas- Mouse Allen Institute ABC Atlas CNS MicroRNA Profiles Washington University School of Medicine, St. Louis CNS MicroRNA Profiles Other Teklad irradiated S-2335 mouse breeder diet #7904 Inotiv Teklad Diet, Bedding and Enrichment (Continued on next page) iScience 29, 116188, June 19, 2026 e1
Functional Assay:Article Title: Genetic inactivation of Translin/Trax RNase disrupts miRNAs, hippocampal synaptic plasticity, and memory.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins miRVana miRNA Isolation Kit with phenol Thermo Fisher Scientific Cat # AM1560 DNase I Zymo Cat # E1010 Illumina TruSeq Small RNA Library Preparation Kit Illumina Cat # RS-200 Illumina Stranded mRNA Library Preparation Kit Illumina Cat # 20040532 iScript cDNA Synthesis Kit Bio-Rad Cat # 1708890 SYBRTM Green Universal Master Mix Thermo Fisher Cat # 4309155 Deposited data Trax miRNA sequencing data This study [Gene Expression Omnibus (GEO)]: [GSE300964] Trax mRNA sequencing data This study [Gene Expression Omnibus (GEO)]: [GSE300964] Experimental models: Organisms/strains C57BL/6-Tsnax em1Jbar /J Jackson Lab strain # 035903 Oligonucleotides See Table S1 for the qPCR primers Integrated DNA Technology (IDT), Coralville, IA, USA N/A Software and algorithms GraphPad Prism GraphPad N/A BioRender BioRender N/A Adobe Illustrator 2024 Adobe N/A Axon pCLAMP 10 Suite (Clampex and Clampfit) Molecular Devices, CA Axon pCLAMP Partek Flow Partek, Illumina, CA Partek Flow ExpressAnalyst110 Express Analyst ExpressAnalyst Venn Diagram Maker Good Calculators Venn Diagram Maker | Good Calculators STRING111 STRING Consortium 2025 STRING: functional protein association networks Ethovision XT Noldus, Leesburg, VA, USA EthoVision XT | Video tracking software | Noldus BORIS Behavioral Analysis Software Olivier Friard, University of Torino, Italy. .. BORIS miRDB miRNA target prediction and functional annotations miRDB - MicroRNA Target Prediction Database FreezeScan System CleverSys Inc., Reston, VA, USA FreezeScan - CleverSys Inc DAVID Bioinformatics Database NIH, USA DAVID Custom Code for gene expression analysis and visualization Zeru Peterson’s Github page Github-ZP-ABC Allen Brain Cell (ABC) Atlas- Mouse Allen Institute ABC Atlas CNS MicroRNA Profiles Washington University School of Medicine, St. Louis CNS MicroRNA Profiles Other Teklad irradiated S-2335 mouse breeder diet #7904 Inotiv Teklad Diet, Bedding and Enrichment (Continued on next page) iScience 29, 116188, June 19, 2026 e1
Microscopy:
Flow Cytometry:
Imaging:
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