Bicinchoninic Acid Protein Assay:Article Title: Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DAPI Sigma-Aldrich Cat#D9542; CAS: 28718-90-3 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat# 78440 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 Precision Plus Protein Dual Color Standards BioRad Cat# 161-0374 Clarity Western ECL Substrate BioRad Cat# 1705060 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Cat# 34094 Restore Plus Western Blot Stripping Buffer Thermo Fisher Cat# 46428 Critical Commercial Assays TURBO DNA-free kit Thermo Fisher Cat#AM1907 QuantSeq 30 mRNA-Seq Library Prep Kit FWD for Illumina Lexogen Cat#015 Qubit RNA HS Assay Kit Thermo Fisher Cat#Q32852 HS NGS Fragment Kit Agilent Cat#DNF-474 Biomark HD 96.96 DNA Binding Dye Sample/ Loading Kit Fluidigm CatBMK-M10-96.96-EG NextSeq 500/550 High Output Kit Illumina Cat#20024906 Deposited Data Raw and processed RNA-Seq data This study GEO: GSE137482 Experimental Models: Organisms/Strains Mouse: GFAP/EGFP Nolte et al., 2001 N/A Mouse: C57Bl6 The Jackson Laboratory Cat#000664 Oligonucleotides Primers for RT-qPCR analysis; see Data S1 This study N/A Software and Algorithms TrimmomaticSE v0.36 Bolger et al. (2014) http://www.usadellab.org/cms/ ?page=trimmomatic SortMeRNA v2.1 Kopylova et al. (2012) https://bioinfo.lifl.fr/RNA/sortmerna/ STAR v2.5.2b Dobin et al. (2013) https://github.com/alexdobin/STAR htseq-count Anders et al. (2015) https://htseq.readthedocs.io/en/ release_0.11.1/count.html DESeq2 v1.16.1 Love et al. (2014) http://bioconductor.org/packages/release/ bioc/html/DESeq2.html GSEA Subramanian et al. (2005) https://www.gsea-msigdb.org/gsea/index.jsp Cytoscape v3.5.1 Shannon et al. (2003) https://cytoscape.org/ ClueGO Bindea et al. (2009) http://apps.cytoscape.org/apps/cluego Enrichment Map Merico et al. (2010) http://apps.cytoscape.org/apps/ enrichmentmap R v3.6.0 https://www.r-project.org/ N/A markerGeneProfile Mancarci et al. (2017) https://github.com/PavlidisLab/ markerGeneProfile CIBERSORT Newman et al. (2015) https://cibersort.stanford.edu/ lmerTest v3.1 Kuznetsova et al. (2017) https://cran.r-project.org/web/packages/ lmerTest/index.html WGCNA Langfelder and Horvath (2008) https://horvath.genetics.ucla.edu/html/ CoexpressionNetwork/Rpackages/WGCNA/ iRegulon Janky et al. (2014) http://iregulon.aertslab.org/ Real-Time PCR analysis software v4.1.3 Fluidigm https://www.fluidigm.com/ GenEx qPCR analysis software v6.0.1 MultiD Analyses AB https://multid.se/genex/ (Continued on next page) e2 Cell Reports 31, 107777, June 16, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER GraphPad Prism GraphPad https://www.graphpad.com/scientific- software/prism/ ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ Other 96.96 Dynamic Array chip for Gene Expression Fluidigm Cat#BMK-M-96.96
Western Blot:Article Title: Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DAPI Sigma-Aldrich Cat#D9542; CAS: 28718-90-3 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat# 78440 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 Precision Plus Protein Dual Color Standards BioRad Cat# 161-0374 Clarity Western ECL Substrate BioRad Cat# 1705060 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Cat# 34094 Restore Plus Western Blot Stripping Buffer Thermo Fisher Cat# 46428 Critical Commercial Assays TURBO DNA-free kit Thermo Fisher Cat#AM1907 QuantSeq 30 mRNA-Seq Library Prep Kit FWD for Illumina Lexogen Cat#015 Qubit RNA HS Assay Kit Thermo Fisher Cat#Q32852 HS NGS Fragment Kit Agilent Cat#DNF-474 Biomark HD 96.96 DNA Binding Dye Sample/ Loading Kit Fluidigm CatBMK-M10-96.96-EG NextSeq 500/550 High Output Kit Illumina Cat#20024906 Deposited Data Raw and processed RNA-Seq data This study GEO: GSE137482 Experimental Models: Organisms/Strains Mouse: GFAP/EGFP Nolte et al., 2001 N/A Mouse: C57Bl6 The Jackson Laboratory Cat#000664 Oligonucleotides Primers for RT-qPCR analysis; see Data S1 This study N/A Software and Algorithms TrimmomaticSE v0.36 Bolger et al. (2014) http://www.usadellab.org/cms/ ?page=trimmomatic SortMeRNA v2.1 Kopylova et al. (2012) https://bioinfo.lifl.fr/RNA/sortmerna/ STAR v2.5.2b Dobin et al. (2013) https://github.com/alexdobin/STAR htseq-count Anders et al. (2015) https://htseq.readthedocs.io/en/ release_0.11.1/count.html DESeq2 v1.16.1 Love et al. (2014) http://bioconductor.org/packages/release/ bioc/html/DESeq2.html GSEA Subramanian et al. (2005) https://www.gsea-msigdb.org/gsea/index.jsp Cytoscape v3.5.1 Shannon et al. (2003) https://cytoscape.org/ ClueGO Bindea et al. (2009) http://apps.cytoscape.org/apps/cluego Enrichment Map Merico et al. (2010) http://apps.cytoscape.org/apps/ enrichmentmap R v3.6.0 https://www.r-project.org/ N/A markerGeneProfile Mancarci et al. (2017) https://github.com/PavlidisLab/ markerGeneProfile CIBERSORT Newman et al. (2015) https://cibersort.stanford.edu/ lmerTest v3.1 Kuznetsova et al. (2017) https://cran.r-project.org/web/packages/ lmerTest/index.html WGCNA Langfelder and Horvath (2008) https://horvath.genetics.ucla.edu/html/ CoexpressionNetwork/Rpackages/WGCNA/ iRegulon Janky et al. (2014) http://iregulon.aertslab.org/ Real-Time PCR analysis software v4.1.3 Fluidigm https://www.fluidigm.com/ GenEx qPCR analysis software v6.0.1 MultiD Analyses AB https://multid.se/genex/ (Continued on next page) e2 Cell Reports 31, 107777, June 16, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER GraphPad Prism GraphPad https://www.graphpad.com/scientific- software/prism/ ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ Other 96.96 Dynamic Array chip for Gene Expression Fluidigm Cat#BMK-M-96.96
Stripping:Article Title: Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DAPI Sigma-Aldrich Cat#D9542; CAS: 28718-90-3 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat# 78440 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 Precision Plus Protein Dual Color Standards BioRad Cat# 161-0374 Clarity Western ECL Substrate BioRad Cat# 1705060 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Cat# 34094 Restore Plus Western Blot Stripping Buffer Thermo Fisher Cat# 46428 Critical Commercial Assays TURBO DNA-free kit Thermo Fisher Cat#AM1907 QuantSeq 30 mRNA-Seq Library Prep Kit FWD for Illumina Lexogen Cat#015 Qubit RNA HS Assay Kit Thermo Fisher Cat#Q32852 HS NGS Fragment Kit Agilent Cat#DNF-474 Biomark HD 96.96 DNA Binding Dye Sample/ Loading Kit Fluidigm CatBMK-M10-96.96-EG NextSeq 500/550 High Output Kit Illumina Cat#20024906 Deposited Data Raw and processed RNA-Seq data This study GEO: GSE137482 Experimental Models: Organisms/Strains Mouse: GFAP/EGFP Nolte et al., 2001 N/A Mouse: C57Bl6 The Jackson Laboratory Cat#000664 Oligonucleotides Primers for RT-qPCR analysis; see Data S1 This study N/A Software and Algorithms TrimmomaticSE v0.36 Bolger et al. (2014) http://www.usadellab.org/cms/ ?page=trimmomatic SortMeRNA v2.1 Kopylova et al. (2012) https://bioinfo.lifl.fr/RNA/sortmerna/ STAR v2.5.2b Dobin et al. (2013) https://github.com/alexdobin/STAR htseq-count Anders et al. (2015) https://htseq.readthedocs.io/en/ release_0.11.1/count.html DESeq2 v1.16.1 Love et al. (2014) http://bioconductor.org/packages/release/ bioc/html/DESeq2.html GSEA Subramanian et al. (2005) https://www.gsea-msigdb.org/gsea/index.jsp Cytoscape v3.5.1 Shannon et al. (2003) https://cytoscape.org/ ClueGO Bindea et al. (2009) http://apps.cytoscape.org/apps/cluego Enrichment Map Merico et al. (2010) http://apps.cytoscape.org/apps/ enrichmentmap R v3.6.0 https://www.r-project.org/ N/A markerGeneProfile Mancarci et al. (2017) https://github.com/PavlidisLab/ markerGeneProfile CIBERSORT Newman et al. (2015) https://cibersort.stanford.edu/ lmerTest v3.1 Kuznetsova et al. (2017) https://cran.r-project.org/web/packages/ lmerTest/index.html WGCNA Langfelder and Horvath (2008) https://horvath.genetics.ucla.edu/html/ CoexpressionNetwork/Rpackages/WGCNA/ iRegulon Janky et al. (2014) http://iregulon.aertslab.org/ Real-Time PCR analysis software v4.1.3 Fluidigm https://www.fluidigm.com/ GenEx qPCR analysis software v6.0.1 MultiD Analyses AB https://multid.se/genex/ (Continued on next page) e2 Cell Reports 31, 107777, June 16, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER GraphPad Prism GraphPad https://www.graphpad.com/scientific- software/prism/ ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ Other 96.96 Dynamic Array chip for Gene Expression Fluidigm Cat#BMK-M-96.96
RNA HS Assay:Article Title: Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DAPI Sigma-Aldrich Cat#D9542; CAS: 28718-90-3 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat# 78440 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 Precision Plus Protein Dual Color Standards BioRad Cat# 161-0374 Clarity Western ECL Substrate BioRad Cat# 1705060 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Cat# 34094 Restore Plus Western Blot Stripping Buffer Thermo Fisher Cat# 46428 Critical Commercial Assays TURBO DNA-free kit Thermo Fisher Cat#AM1907 QuantSeq 30 mRNA-Seq Library Prep Kit FWD for Illumina Lexogen Cat#015 Qubit RNA HS Assay Kit Thermo Fisher Cat#Q32852 HS NGS Fragment Kit Agilent Cat#DNF-474 Biomark HD 96.96 DNA Binding Dye Sample/ Loading Kit Fluidigm CatBMK-M10-96.96-EG NextSeq 500/550 High Output Kit Illumina Cat#20024906 Deposited Data Raw and processed RNA-Seq data This study GEO: GSE137482 Experimental Models: Organisms/Strains Mouse: GFAP/EGFP Nolte et al., 2001 N/A Mouse: C57Bl6 The Jackson Laboratory Cat#000664 Oligonucleotides Primers for RT-qPCR analysis; see Data S1 This study N/A Software and Algorithms TrimmomaticSE v0.36 Bolger et al. (2014) http://www.usadellab.org/cms/ ?page=trimmomatic SortMeRNA v2.1 Kopylova et al. (2012) https://bioinfo.lifl.fr/RNA/sortmerna/ STAR v2.5.2b Dobin et al. (2013) https://github.com/alexdobin/STAR htseq-count Anders et al. (2015) https://htseq.readthedocs.io/en/ release_0.11.1/count.html DESeq2 v1.16.1 Love et al. (2014) http://bioconductor.org/packages/release/ bioc/html/DESeq2.html GSEA Subramanian et al. (2005) https://www.gsea-msigdb.org/gsea/index.jsp Cytoscape v3.5.1 Shannon et al. (2003) https://cytoscape.org/ ClueGO Bindea et al. (2009) http://apps.cytoscape.org/apps/cluego Enrichment Map Merico et al. (2010) http://apps.cytoscape.org/apps/ enrichmentmap R v3.6.0 https://www.r-project.org/ N/A markerGeneProfile Mancarci et al. (2017) https://github.com/PavlidisLab/ markerGeneProfile CIBERSORT Newman et al. (2015) https://cibersort.stanford.edu/ lmerTest v3.1 Kuznetsova et al. (2017) https://cran.r-project.org/web/packages/ lmerTest/index.html WGCNA Langfelder and Horvath (2008) https://horvath.genetics.ucla.edu/html/ CoexpressionNetwork/Rpackages/WGCNA/ iRegulon Janky et al. (2014) http://iregulon.aertslab.org/ Real-Time PCR analysis software v4.1.3 Fluidigm https://www.fluidigm.com/ GenEx qPCR analysis software v6.0.1 MultiD Analyses AB https://multid.se/genex/ (Continued on next page) e2 Cell Reports 31, 107777, June 16, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER GraphPad Prism GraphPad https://www.graphpad.com/scientific- software/prism/ ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ Other 96.96 Dynamic Array chip for Gene Expression Fluidigm Cat#BMK-M-96.96
Next-Generation Sequencing:Article Title: Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DAPI Sigma-Aldrich Cat#D9542; CAS: 28718-90-3 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat# 78440 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 Precision Plus Protein Dual Color Standards BioRad Cat# 161-0374 Clarity Western ECL Substrate BioRad Cat# 1705060 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Cat# 34094 Restore Plus Western Blot Stripping Buffer Thermo Fisher Cat# 46428 Critical Commercial Assays TURBO DNA-free kit Thermo Fisher Cat#AM1907 QuantSeq 30 mRNA-Seq Library Prep Kit FWD for Illumina Lexogen Cat#015 Qubit RNA HS Assay Kit Thermo Fisher Cat#Q32852 HS NGS Fragment Kit Agilent Cat#DNF-474 Biomark HD 96.96 DNA Binding Dye Sample/ Loading Kit Fluidigm CatBMK-M10-96.96-EG NextSeq 500/550 High Output Kit Illumina Cat#20024906 Deposited Data Raw and processed RNA-Seq data This study GEO: GSE137482 Experimental Models: Organisms/Strains Mouse: GFAP/EGFP Nolte et al., 2001 N/A Mouse: C57Bl6 The Jackson Laboratory Cat#000664 Oligonucleotides Primers for RT-qPCR analysis; see Data S1 This study N/A Software and Algorithms TrimmomaticSE v0.36 Bolger et al. (2014) http://www.usadellab.org/cms/ ?page=trimmomatic SortMeRNA v2.1 Kopylova et al. (2012) https://bioinfo.lifl.fr/RNA/sortmerna/ STAR v2.5.2b Dobin et al. (2013) https://github.com/alexdobin/STAR htseq-count Anders et al. (2015) https://htseq.readthedocs.io/en/ release_0.11.1/count.html DESeq2 v1.16.1 Love et al. (2014) http://bioconductor.org/packages/release/ bioc/html/DESeq2.html GSEA Subramanian et al. (2005) https://www.gsea-msigdb.org/gsea/index.jsp Cytoscape v3.5.1 Shannon et al. (2003) https://cytoscape.org/ ClueGO Bindea et al. (2009) http://apps.cytoscape.org/apps/cluego Enrichment Map Merico et al. (2010) http://apps.cytoscape.org/apps/ enrichmentmap R v3.6.0 https://www.r-project.org/ N/A markerGeneProfile Mancarci et al. (2017) https://github.com/PavlidisLab/ markerGeneProfile CIBERSORT Newman et al. (2015) https://cibersort.stanford.edu/ lmerTest v3.1 Kuznetsova et al. (2017) https://cran.r-project.org/web/packages/ lmerTest/index.html WGCNA Langfelder and Horvath (2008) https://horvath.genetics.ucla.edu/html/ CoexpressionNetwork/Rpackages/WGCNA/ iRegulon Janky et al. (2014) http://iregulon.aertslab.org/ Real-Time PCR analysis software v4.1.3 Fluidigm https://www.fluidigm.com/ GenEx qPCR analysis software v6.0.1 MultiD Analyses AB https://multid.se/genex/ (Continued on next page) e2 Cell Reports 31, 107777, June 16, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER GraphPad Prism GraphPad https://www.graphpad.com/scientific- software/prism/ ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ Other 96.96 Dynamic Array chip for Gene Expression Fluidigm Cat#BMK-M-96.96
Binding Assay:Article Title: Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DAPI Sigma-Aldrich Cat#D9542; CAS: 28718-90-3 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat# 78440 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 Precision Plus Protein Dual Color Standards BioRad Cat# 161-0374 Clarity Western ECL Substrate BioRad Cat# 1705060 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Cat# 34094 Restore Plus Western Blot Stripping Buffer Thermo Fisher Cat# 46428 Critical Commercial Assays TURBO DNA-free kit Thermo Fisher Cat#AM1907 QuantSeq 30 mRNA-Seq Library Prep Kit FWD for Illumina Lexogen Cat#015 Qubit RNA HS Assay Kit Thermo Fisher Cat#Q32852 HS NGS Fragment Kit Agilent Cat#DNF-474 Biomark HD 96.96 DNA Binding Dye Sample/ Loading Kit Fluidigm CatBMK-M10-96.96-EG NextSeq 500/550 High Output Kit Illumina Cat#20024906 Deposited Data Raw and processed RNA-Seq data This study GEO: GSE137482 Experimental Models: Organisms/Strains Mouse: GFAP/EGFP Nolte et al., 2001 N/A Mouse: C57Bl6 The Jackson Laboratory Cat#000664 Oligonucleotides Primers for RT-qPCR analysis; see Data S1 This study N/A Software and Algorithms TrimmomaticSE v0.36 Bolger et al. (2014) http://www.usadellab.org/cms/ ?page=trimmomatic SortMeRNA v2.1 Kopylova et al. (2012) https://bioinfo.lifl.fr/RNA/sortmerna/ STAR v2.5.2b Dobin et al. (2013) https://github.com/alexdobin/STAR htseq-count Anders et al. (2015) https://htseq.readthedocs.io/en/ release_0.11.1/count.html DESeq2 v1.16.1 Love et al. (2014) http://bioconductor.org/packages/release/ bioc/html/DESeq2.html GSEA Subramanian et al. (2005) https://www.gsea-msigdb.org/gsea/index.jsp Cytoscape v3.5.1 Shannon et al. (2003) https://cytoscape.org/ ClueGO Bindea et al. (2009) http://apps.cytoscape.org/apps/cluego Enrichment Map Merico et al. (2010) http://apps.cytoscape.org/apps/ enrichmentmap R v3.6.0 https://www.r-project.org/ N/A markerGeneProfile Mancarci et al. (2017) https://github.com/PavlidisLab/ markerGeneProfile CIBERSORT Newman et al. (2015) https://cibersort.stanford.edu/ lmerTest v3.1 Kuznetsova et al. (2017) https://cran.r-project.org/web/packages/ lmerTest/index.html WGCNA Langfelder and Horvath (2008) https://horvath.genetics.ucla.edu/html/ CoexpressionNetwork/Rpackages/WGCNA/ iRegulon Janky et al. (2014) http://iregulon.aertslab.org/ Real-Time PCR analysis software v4.1.3 Fluidigm https://www.fluidigm.com/ GenEx qPCR analysis software v6.0.1 MultiD Analyses AB https://multid.se/genex/ (Continued on next page) e2 Cell Reports 31, 107777, June 16, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER GraphPad Prism GraphPad https://www.graphpad.com/scientific- software/prism/ ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ Other 96.96 Dynamic Array chip for Gene Expression Fluidigm Cat#BMK-M-96.96
Article Title: Impaired mRNA splicing and proteostasis in preadipocytes in obesity-related metabolic disease
Article Snippet: Chemical compound, drug , Urea , Sigma-Aldrich , U1205 , . .. Commercial assay or kit , 96.96 DNA Binding Dye Sample / Loading Kit , Fluidigm , BMK-M10-96.96-EG , . .. Commercial assay or kit , AllPrep DNA/RNA/Protein Mini Kit , Qiagen , 80,004 , .
Article Title: High-throughput quantification of camelid cytokine mRNA expression in PBMCs by microfluidic qPCR technology
Article Snippet: Pre-amplified products were treated with Exonuclease I (New England Biolabs, Ipswich, USA) for 30 min at 37°C to eliminate the carryover of unincorporated primers. .. The 96.96 Dynamic Array IFCs, the 96.96 DNA Binding Dye Sample/Loading Kit (Fluidigm Corporation, South San Francisco, USA) was prepared according to the manufacturer’s instructions. .. The 96.96 Dynamic Array IFCs, the 96.96 DNA Binding Dye Sample/Loading Kit (Fluidigm Corporation, South San Francisco, USA) was prepared according to the manufacturer’s instructions.
Article Title: Quantification of camelid cytokine mRNA expression in PBMCs by microfluidic qPCR technology.
Article Snippet: Camelids are economically and socially important in several parts of the world and might carry pathogens with epizootic or zoonotic potential.. However, biological research in these species is limited due to lack of reagents.. Here, we developed RT-qPCR assays to quantify a panel of camelid innate and adaptive immune response genes, which can be monitored in a single run.
RNA sequencing:Article Title: Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DAPI Sigma-Aldrich Cat#D9542; CAS: 28718-90-3 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat# 78440 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 Precision Plus Protein Dual Color Standards BioRad Cat# 161-0374 Clarity Western ECL Substrate BioRad Cat# 1705060 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Cat# 34094 Restore Plus Western Blot Stripping Buffer Thermo Fisher Cat# 46428 Critical Commercial Assays TURBO DNA-free kit Thermo Fisher Cat#AM1907 QuantSeq 30 mRNA-Seq Library Prep Kit FWD for Illumina Lexogen Cat#015 Qubit RNA HS Assay Kit Thermo Fisher Cat#Q32852 HS NGS Fragment Kit Agilent Cat#DNF-474 Biomark HD 96.96 DNA Binding Dye Sample/ Loading Kit Fluidigm CatBMK-M10-96.96-EG NextSeq 500/550 High Output Kit Illumina Cat#20024906 Deposited Data Raw and processed RNA-Seq data This study GEO: GSE137482 Experimental Models: Organisms/Strains Mouse: GFAP/EGFP Nolte et al., 2001 N/A Mouse: C57Bl6 The Jackson Laboratory Cat#000664 Oligonucleotides Primers for RT-qPCR analysis; see Data S1 This study N/A Software and Algorithms TrimmomaticSE v0.36 Bolger et al. (2014) http://www.usadellab.org/cms/ ?page=trimmomatic SortMeRNA v2.1 Kopylova et al. (2012) https://bioinfo.lifl.fr/RNA/sortmerna/ STAR v2.5.2b Dobin et al. (2013) https://github.com/alexdobin/STAR htseq-count Anders et al. (2015) https://htseq.readthedocs.io/en/ release_0.11.1/count.html DESeq2 v1.16.1 Love et al. (2014) http://bioconductor.org/packages/release/ bioc/html/DESeq2.html GSEA Subramanian et al. (2005) https://www.gsea-msigdb.org/gsea/index.jsp Cytoscape v3.5.1 Shannon et al. (2003) https://cytoscape.org/ ClueGO Bindea et al. (2009) http://apps.cytoscape.org/apps/cluego Enrichment Map Merico et al. (2010) http://apps.cytoscape.org/apps/ enrichmentmap R v3.6.0 https://www.r-project.org/ N/A markerGeneProfile Mancarci et al. (2017) https://github.com/PavlidisLab/ markerGeneProfile CIBERSORT Newman et al. (2015) https://cibersort.stanford.edu/ lmerTest v3.1 Kuznetsova et al. (2017) https://cran.r-project.org/web/packages/ lmerTest/index.html WGCNA Langfelder and Horvath (2008) https://horvath.genetics.ucla.edu/html/ CoexpressionNetwork/Rpackages/WGCNA/ iRegulon Janky et al. (2014) http://iregulon.aertslab.org/ Real-Time PCR analysis software v4.1.3 Fluidigm https://www.fluidigm.com/ GenEx qPCR analysis software v6.0.1 MultiD Analyses AB https://multid.se/genex/ (Continued on next page) e2 Cell Reports 31, 107777, June 16, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER GraphPad Prism GraphPad https://www.graphpad.com/scientific- software/prism/ ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ Other 96.96 Dynamic Array chip for Gene Expression Fluidigm Cat#BMK-M-96.96
Quantitative RT-PCR:Article Title: Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DAPI Sigma-Aldrich Cat#D9542; CAS: 28718-90-3 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat# 78440 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 Precision Plus Protein Dual Color Standards BioRad Cat# 161-0374 Clarity Western ECL Substrate BioRad Cat# 1705060 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Cat# 34094 Restore Plus Western Blot Stripping Buffer Thermo Fisher Cat# 46428 Critical Commercial Assays TURBO DNA-free kit Thermo Fisher Cat#AM1907 QuantSeq 30 mRNA-Seq Library Prep Kit FWD for Illumina Lexogen Cat#015 Qubit RNA HS Assay Kit Thermo Fisher Cat#Q32852 HS NGS Fragment Kit Agilent Cat#DNF-474 Biomark HD 96.96 DNA Binding Dye Sample/ Loading Kit Fluidigm CatBMK-M10-96.96-EG NextSeq 500/550 High Output Kit Illumina Cat#20024906 Deposited Data Raw and processed RNA-Seq data This study GEO: GSE137482 Experimental Models: Organisms/Strains Mouse: GFAP/EGFP Nolte et al., 2001 N/A Mouse: C57Bl6 The Jackson Laboratory Cat#000664 Oligonucleotides Primers for RT-qPCR analysis; see Data S1 This study N/A Software and Algorithms TrimmomaticSE v0.36 Bolger et al. (2014) http://www.usadellab.org/cms/ ?page=trimmomatic SortMeRNA v2.1 Kopylova et al. (2012) https://bioinfo.lifl.fr/RNA/sortmerna/ STAR v2.5.2b Dobin et al. (2013) https://github.com/alexdobin/STAR htseq-count Anders et al. (2015) https://htseq.readthedocs.io/en/ release_0.11.1/count.html DESeq2 v1.16.1 Love et al. (2014) http://bioconductor.org/packages/release/ bioc/html/DESeq2.html GSEA Subramanian et al. (2005) https://www.gsea-msigdb.org/gsea/index.jsp Cytoscape v3.5.1 Shannon et al. (2003) https://cytoscape.org/ ClueGO Bindea et al. (2009) http://apps.cytoscape.org/apps/cluego Enrichment Map Merico et al. (2010) http://apps.cytoscape.org/apps/ enrichmentmap R v3.6.0 https://www.r-project.org/ N/A markerGeneProfile Mancarci et al. (2017) https://github.com/PavlidisLab/ markerGeneProfile CIBERSORT Newman et al. (2015) https://cibersort.stanford.edu/ lmerTest v3.1 Kuznetsova et al. (2017) https://cran.r-project.org/web/packages/ lmerTest/index.html WGCNA Langfelder and Horvath (2008) https://horvath.genetics.ucla.edu/html/ CoexpressionNetwork/Rpackages/WGCNA/ iRegulon Janky et al. (2014) http://iregulon.aertslab.org/ Real-Time PCR analysis software v4.1.3 Fluidigm https://www.fluidigm.com/ GenEx qPCR analysis software v6.0.1 MultiD Analyses AB https://multid.se/genex/ (Continued on next page) e2 Cell Reports 31, 107777, June 16, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER GraphPad Prism GraphPad https://www.graphpad.com/scientific- software/prism/ ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ Other 96.96 Dynamic Array chip for Gene Expression Fluidigm Cat#BMK-M-96.96
Software:Article Title: Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DAPI Sigma-Aldrich Cat#D9542; CAS: 28718-90-3 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat# 78440 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 Precision Plus Protein Dual Color Standards BioRad Cat# 161-0374 Clarity Western ECL Substrate BioRad Cat# 1705060 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Cat# 34094 Restore Plus Western Blot Stripping Buffer Thermo Fisher Cat# 46428 Critical Commercial Assays TURBO DNA-free kit Thermo Fisher Cat#AM1907 QuantSeq 30 mRNA-Seq Library Prep Kit FWD for Illumina Lexogen Cat#015 Qubit RNA HS Assay Kit Thermo Fisher Cat#Q32852 HS NGS Fragment Kit Agilent Cat#DNF-474 Biomark HD 96.96 DNA Binding Dye Sample/ Loading Kit Fluidigm CatBMK-M10-96.96-EG NextSeq 500/550 High Output Kit Illumina Cat#20024906 Deposited Data Raw and processed RNA-Seq data This study GEO: GSE137482 Experimental Models: Organisms/Strains Mouse: GFAP/EGFP Nolte et al., 2001 N/A Mouse: C57Bl6 The Jackson Laboratory Cat#000664 Oligonucleotides Primers for RT-qPCR analysis; see Data S1 This study N/A Software and Algorithms TrimmomaticSE v0.36 Bolger et al. (2014) http://www.usadellab.org/cms/ ?page=trimmomatic SortMeRNA v2.1 Kopylova et al. (2012) https://bioinfo.lifl.fr/RNA/sortmerna/ STAR v2.5.2b Dobin et al. (2013) https://github.com/alexdobin/STAR htseq-count Anders et al. (2015) https://htseq.readthedocs.io/en/ release_0.11.1/count.html DESeq2 v1.16.1 Love et al. (2014) http://bioconductor.org/packages/release/ bioc/html/DESeq2.html GSEA Subramanian et al. (2005) https://www.gsea-msigdb.org/gsea/index.jsp Cytoscape v3.5.1 Shannon et al. (2003) https://cytoscape.org/ ClueGO Bindea et al. (2009) http://apps.cytoscape.org/apps/cluego Enrichment Map Merico et al. (2010) http://apps.cytoscape.org/apps/ enrichmentmap R v3.6.0 https://www.r-project.org/ N/A markerGeneProfile Mancarci et al. (2017) https://github.com/PavlidisLab/ markerGeneProfile CIBERSORT Newman et al. (2015) https://cibersort.stanford.edu/ lmerTest v3.1 Kuznetsova et al. (2017) https://cran.r-project.org/web/packages/ lmerTest/index.html WGCNA Langfelder and Horvath (2008) https://horvath.genetics.ucla.edu/html/ CoexpressionNetwork/Rpackages/WGCNA/ iRegulon Janky et al. (2014) http://iregulon.aertslab.org/ Real-Time PCR analysis software v4.1.3 Fluidigm https://www.fluidigm.com/ GenEx qPCR analysis software v6.0.1 MultiD Analyses AB https://multid.se/genex/ (Continued on next page) e2 Cell Reports 31, 107777, June 16, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER GraphPad Prism GraphPad https://www.graphpad.com/scientific- software/prism/ ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ Other 96.96 Dynamic Array chip for Gene Expression Fluidigm Cat#BMK-M-96.96
Real-time Polymerase Chain Reaction:Article Title: Decoding the Transcriptional Response to Ischemic Stroke in Young and Aged Mouse Brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER DAPI Sigma-Aldrich Cat#D9542; CAS: 28718-90-3 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat# 78440 Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 Precision Plus Protein Dual Color Standards BioRad Cat# 161-0374 Clarity Western ECL Substrate BioRad Cat# 1705060 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Cat# 34094 Restore Plus Western Blot Stripping Buffer Thermo Fisher Cat# 46428 Critical Commercial Assays TURBO DNA-free kit Thermo Fisher Cat#AM1907 QuantSeq 30 mRNA-Seq Library Prep Kit FWD for Illumina Lexogen Cat#015 Qubit RNA HS Assay Kit Thermo Fisher Cat#Q32852 HS NGS Fragment Kit Agilent Cat#DNF-474 Biomark HD 96.96 DNA Binding Dye Sample/ Loading Kit Fluidigm CatBMK-M10-96.96-EG NextSeq 500/550 High Output Kit Illumina Cat#20024906 Deposited Data Raw and processed RNA-Seq data This study GEO: GSE137482 Experimental Models: Organisms/Strains Mouse: GFAP/EGFP Nolte et al., 2001 N/A Mouse: C57Bl6 The Jackson Laboratory Cat#000664 Oligonucleotides Primers for RT-qPCR analysis; see Data S1 This study N/A Software and Algorithms TrimmomaticSE v0.36 Bolger et al. (2014) http://www.usadellab.org/cms/ ?page=trimmomatic SortMeRNA v2.1 Kopylova et al. (2012) https://bioinfo.lifl.fr/RNA/sortmerna/ STAR v2.5.2b Dobin et al. (2013) https://github.com/alexdobin/STAR htseq-count Anders et al. (2015) https://htseq.readthedocs.io/en/ release_0.11.1/count.html DESeq2 v1.16.1 Love et al. (2014) http://bioconductor.org/packages/release/ bioc/html/DESeq2.html GSEA Subramanian et al. (2005) https://www.gsea-msigdb.org/gsea/index.jsp Cytoscape v3.5.1 Shannon et al. (2003) https://cytoscape.org/ ClueGO Bindea et al. (2009) http://apps.cytoscape.org/apps/cluego Enrichment Map Merico et al. (2010) http://apps.cytoscape.org/apps/ enrichmentmap R v3.6.0 https://www.r-project.org/ N/A markerGeneProfile Mancarci et al. (2017) https://github.com/PavlidisLab/ markerGeneProfile CIBERSORT Newman et al. (2015) https://cibersort.stanford.edu/ lmerTest v3.1 Kuznetsova et al. (2017) https://cran.r-project.org/web/packages/ lmerTest/index.html WGCNA Langfelder and Horvath (2008) https://horvath.genetics.ucla.edu/html/ CoexpressionNetwork/Rpackages/WGCNA/ iRegulon Janky et al. (2014) http://iregulon.aertslab.org/ Real-Time PCR analysis software v4.1.3 Fluidigm https://www.fluidigm.com/ GenEx qPCR analysis software v6.0.1 MultiD Analyses AB https://multid.se/genex/ (Continued on next page) e2 Cell Reports 31, 107777, June 16, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER GraphPad Prism GraphPad https://www.graphpad.com/scientific- software/prism/ ImageJ Schneider et al., 2012 https://imagej.nih.gov/ij/ Other 96.96 Dynamic Array chip for Gene Expression Fluidigm Cat#BMK-M-96.96
other:Article Title: Comparative immune profiling of acute respiratory distress syndrome patients with or without SARS-CoV-2 infection.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER CD117 (104D2), Purified BioLegend Cat# 105814; RRID: AB_313223 CCR4 (L291H4), Purified BioLegend Cat# 359402; RRID: AB_2562364 CD161 (HP-3G10), Purified BioLegend Cat# 339919; RRID: AB_2562836 CD185 (J252D4), Purified BioLegend Cat# 356902; RRID: AB_2561811 RORgt (AFKJS-9), Purified Thermo Fisher Scientific Cat# 14-6988-82; RRID: AB_1834475 CD294 (BM16), Purified BioLegend Cat# 350102, RRID: AB_10639863 LAG-3 (7H2C65), Purified BioLegend Cat# 369202; RRID: AB_2616877 CTLA-4 (L3D10), Purified BioLegend Cat# 349902; RRID: AB_10642827 PD-1 (EH12.2H7), Purified BioLegend Cat# 329941; RRID: AB_2563734 Tim-3 (F38-2E2), Purified BioLegend Cat# 345019; RRID: AB_2563790 CD127 (A019D5), Purified BioLegend Cat# 351337; RRID: AB_2563715 Bcl-6 (k112-91), Purified BD Biosciences Cat# 561520; RRID: AB_10713172 T-bet (4B10), Purified BioLegend Cat# 644825; RRID: AB_2563788 CD45RO (UCHL1), Purified BioLegend Cat# 304239; RRID: AB_2563752 CD56 (HCD56), Purified BioLegend Cat# 318302; RRID: AB_604092 Ki-67 (Ki-67), Purified BioLegend Cat# 350523; RRID: AB_2562838 CD44 (BJ18), Purified BioLegend Cat# 338802; RRID: AB_1501199 CD45 (HI30), 89Y Fluidigm Cat# 3089003; RRID: AB_2661851 CD326 (9C4), Purified BioLegend Cat# 324229; RRID: AB_2563742 CD19 (HIB19), Purified BioLegend Cat# 302202; RRID: AB_314232 HLA-DR (10.1), Purified BioLegend Cat# 307602; RRID: AB_314680 CD31 (WM59), Purified BioLegend Cat# 303127; RRID: AB_2563740 CD16 (B73.1), Purified BioLegend Cat# 360702; RRID: AB_2562693 CD64 (L243), Purified BioLegend Cat# 305029; RRID: AB_2563759 Chemicals, peptides, and recombinant proteins EQ Four Element Calibration Beads Fluidigm Cat# 201078 Antibody Stabilizer PBS Candor Bioscience Cat# 131050 Bond-Breaker TCEP Solution Thermo Fisher Scientific Cat# 77720 Cell-ID Intercalator-Ir Fluidigm Cat# 201192B Cell-ID Cisplatin-198Pt Fluidigm Cat# 201198 Cell Acquisition Solution Fluidigm Cat# 201240 Critical commercial assays Transcription factor staining buffer set Miltenyi Biotec Cat# 130-122-981 Maxpar X8 Multimetal Antibody Labeling Kit Fluidigm Cat# 201300 Preamp Master Mix Fluidigm Cat# 100-5580 Reverse Transcription Master Mix Fluidigm Cat# 100-6298 TaqMan Universal PCR Master Mix (2X) Life Technologies Cat# PN 4304437 96.96 DNA Binding Dye Sample/Loading Kit—10 IFCs Fluidigm Cat# BMK-M10-96.96-EG Deposited data CyTOF data Chevrier et al.15 https://doi.org/10.1016/j.xcrm.2020.
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