Extraction:Article Title: StarD5 levels of expression correlate with onset and progression of steatosis and liver fibrosis.
Article Snippet: Corresponding author: Daniel Rodriguez-Agudo, Email: daniel.rodriguezagudo@vcuhealth.org 9 10 11 Abbreviations: 26-HC, (25R)26-hydroxycholesterol, 3βHCA, 3β-Hydroxy-5-cholesten-(25R)26-oic 12 acid, ACC, Acetyl CoA-carboxylase; ER, endoplasmic reticulum; FAS, Fatty Acids synthetase; HMG13 CoA, 3-hydroxy-3-methylglutaryl coenzyme A; HOMA-IR, Homeostatic Model Assessment for Insulin 14 Resistance; HRP, horseradish peroxidase; Apo, apolipoprotein; LXR, liver X receptor; MTTP, 15 microsomal triglyceride transfer protein; MASLD, Metabolic Dysfunction Associated Steatotic Liver 16 Disease; MASH, Metabolic Associated Steatohepatitis; PM, plasma membrane; qRT-PCR, quantitative 17 RT-PCR; SREBP, Sterol Regulatory-Element Binding Protein; StarD, steroidogenic acute regulatory18 related lipid transfer domain; TG; triglyceride; TM6SF2, transmembrane 6 superfamily member 2; UPR, 19 unfolded protein response; VLDL, very low-density lipoprotein; WD, Western diet; WT, wild type.. 20 21
Amplex Red Cholesterol Assay:
Enzymatic Assay:Article Title: COP9 signalosome is required for adipose tissue maintenance and metabolic health
Article Snippet: Fluorescent images were captured with a Fluorescence Microscope (BZ-X710, KEYENCE, Osaka, Japan). .. Enzymatic assay kits were used to determine serum nonesterified fatty acids (NEFAs) (WAKO NEFA analysis kit (NEFA-HR(2); Wako Pure Chemical Industries), glycerol (free glycerol reagent, Cat#F6428, MilliporeSigma, Burlington, MA), triglycerides (Infinity Triglycerides Assay Kit, Cat#TR-22421, Thermo Fisher Scientific) and cholesterol (Infinity Cholesterol Assay Kit, Cat#TR-13421, Thermo Fisher Scientific). .. Plasma insulin (Millipore Sigma, Cat#EZRMI-13K) and leptin (Millipore Sigma, Cat#EZML-82K) levels were measured using enzyme-linked immunosorbent assay kits according to the manufacturer’s protocols.
Article Title: COP9 signalosome is required for adipose tissue maintenance and metabolic health.
Article Snippet: Fluorescent images were captured with a Fluorescence Microscope (BZ-X710, KEYENCE, Osaka, Japan). .. Enzymatic assay kits were used to determine serum nonesterified fatty acids (NEFAs) (WAKO NEFA analysis kit (NEFA-HR(2); Wako Pure Chemical Industries), glycerol (free glycerol reagent, Cat#F6428, MilliporeSigma, Burlington, MA), triglycerides (Infinity Triglycerides Assay Kit, Cat#TR22421, Thermo Fisher Scientific) and cholesterol (Infinity Cholesterol Assay Kit, Cat#TR-13421, Thermo Fisher Scientific). .. Plasma insulin (Millipore Sigma, Cat#EZRMI-13K) and leptin (Millipore Sigma, Cat#EZML-82K) levels were measured using enzyme-linked immunosorbent assay kits according to the manufacturer’s protocols.
Cholesterol Assay:Article Title: COP9 signalosome is required for adipose tissue maintenance and metabolic health
Article Snippet: Fluorescent images were captured with a Fluorescence Microscope (BZ-X710, KEYENCE, Osaka, Japan). .. Enzymatic assay kits were used to determine serum nonesterified fatty acids (NEFAs) (WAKO NEFA analysis kit (NEFA-HR(2); Wako Pure Chemical Industries), glycerol (free glycerol reagent, Cat#F6428, MilliporeSigma, Burlington, MA), triglycerides (Infinity Triglycerides Assay Kit, Cat#TR-22421, Thermo Fisher Scientific) and cholesterol (Infinity Cholesterol Assay Kit, Cat#TR-13421, Thermo Fisher Scientific). .. Plasma insulin (Millipore Sigma, Cat#EZRMI-13K) and leptin (Millipore Sigma, Cat#EZML-82K) levels were measured using enzyme-linked immunosorbent assay kits according to the manufacturer’s protocols.
Article Title: Diurnal transcriptome landscape of a multi-tissue response to time-restricted feeding in mammals.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Infinity Cholesterol assay kit Thermo Scientific #TR13421 Infinity Triglycerides assay kit Thermo Scientific #TR22421 Mouse Insulin ELISA kit Crystal Chem #90080 Mouse Leptin ELISA kit Crystal Chem #90030 Autokit 3-HB kit Wako Diagnostics #417-73501 Quant-iT RNA Assay Kit Thermo Scientific #Q33140 Quant-iT DNA Assay Kit Thermo Scientific #Q33120 TruSeq Stranded mRNA kit Illumina #20020595 Deposited data Raw files for RNA sequencing This paper GSE190389 TMM normalized counts, statistical analyses for differential and rhythmic gene expression, and liver metabolome counts and statistical analyses This paper https://data.mendeley.com/datasets/ wc5wy48x93/draft?a=8aafd31c-bdf94782-bffe-10eccb3dd093 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory #000664 Software and algorithms Prism 6.0 GraphPad Software https://www.graphpad.com R, v4.0.3 R Development Core Team, 2022 https://www.R-project.org/ Rstudio, v1.3.1093 Rstudio: Integrated Development for R, Boston, MA https://www.rstudio.com/ FastQC, v0.11.5 Babraham Bioinformatics, Cambridge, UK https://www.bioinformatics.babraham.ac. uk/projects/fastqc/ STAR v2.5.3a Dobin et al., 201369 https://github.com/alexdobin/STAR HOMER v4.10 Heinz et al., 201070 http://homer.ucsd.edu/homer/ DESeq2 v1.24.0 Love, Huber and Anders, 201471 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html edgeR v3.26.7 Robinson, McCarthy and Smyth, 2010;33 McCarthy, Chen and Smyth, 201272 https://bioconductor.org/packages/ release/bioc/html/edgeR.html Network Analyst Zhou et al., 2019a34 https://www.networkanalyst.ca/ NetworkAnalyst/home.xhtml Morpheus Broad Institute, Cambridge, MA https://software.broadinstitute.org/ morpheus Uwot McInnes, Healy and Melville, 201873 https://github.com/jlmelville/uwot ClusterProfiler Yu et al., 201274 https://guangchuangyu.github.io/software/ clusterProfiler/ Metacycle Wu et al., 201643 https://github.com/gangwug/MetaCycle Metascape Zhou et al., 2019b75 https://metascape.org/gp/index.html#/ main/step1 WebGestaltR v0.3.1 Liao et al., 201976 http://www.webgestalt.org/ PSEA Zhang et al., 201647 https://github.com/ranafi/PSEA (Continued on next page) e1 Cell Metabolism 35, 150–165.e1–e4, January 3, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER g:Profiler Raudvere et al., 201977 https://biit.cs.ut.ee/gprofiler/gost Metaboanalyst v5.0 Pang et al., 202151 https://www.metaboanalyst.ca/ MetaboAnalyst/faces/home.xhtml Other Rodent Diet With 45 kcal% Fat Research Diets, Inc. D12451 Rodent regular chow diet LabDiet 5053 - PicoLab Rodent diet 20 extruded, #3002890-712
Article Title: COP9 signalosome is required for adipose tissue maintenance and metabolic health.
Article Snippet: Fluorescent images were captured with a Fluorescence Microscope (BZ-X710, KEYENCE, Osaka, Japan). .. Enzymatic assay kits were used to determine serum nonesterified fatty acids (NEFAs) (WAKO NEFA analysis kit (NEFA-HR(2); Wako Pure Chemical Industries), glycerol (free glycerol reagent, Cat#F6428, MilliporeSigma, Burlington, MA), triglycerides (Infinity Triglycerides Assay Kit, Cat#TR22421, Thermo Fisher Scientific) and cholesterol (Infinity Cholesterol Assay Kit, Cat#TR-13421, Thermo Fisher Scientific). .. Plasma insulin (Millipore Sigma, Cat#EZRMI-13K) and leptin (Millipore Sigma, Cat#EZML-82K) levels were measured using enzyme-linked immunosorbent assay kits according to the manufacturer’s protocols.
Enzyme-linked Immunosorbent Assay:Article Title: Diurnal transcriptome landscape of a multi-tissue response to time-restricted feeding in mammals.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Infinity Cholesterol assay kit Thermo Scientific #TR13421 Infinity Triglycerides assay kit Thermo Scientific #TR22421 Mouse Insulin ELISA kit Crystal Chem #90080 Mouse Leptin ELISA kit Crystal Chem #90030 Autokit 3-HB kit Wako Diagnostics #417-73501 Quant-iT RNA Assay Kit Thermo Scientific #Q33140 Quant-iT DNA Assay Kit Thermo Scientific #Q33120 TruSeq Stranded mRNA kit Illumina #20020595 Deposited data Raw files for RNA sequencing This paper GSE190389 TMM normalized counts, statistical analyses for differential and rhythmic gene expression, and liver metabolome counts and statistical analyses This paper https://data.mendeley.com/datasets/ wc5wy48x93/draft?a=8aafd31c-bdf94782-bffe-10eccb3dd093 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory #000664 Software and algorithms Prism 6.0 GraphPad Software https://www.graphpad.com R, v4.0.3 R Development Core Team, 2022 https://www.R-project.org/ Rstudio, v1.3.1093 Rstudio: Integrated Development for R, Boston, MA https://www.rstudio.com/ FastQC, v0.11.5 Babraham Bioinformatics, Cambridge, UK https://www.bioinformatics.babraham.ac. uk/projects/fastqc/ STAR v2.5.3a Dobin et al., 201369 https://github.com/alexdobin/STAR HOMER v4.10 Heinz et al., 201070 http://homer.ucsd.edu/homer/ DESeq2 v1.24.0 Love, Huber and Anders, 201471 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html edgeR v3.26.7 Robinson, McCarthy and Smyth, 2010;33 McCarthy, Chen and Smyth, 201272 https://bioconductor.org/packages/ release/bioc/html/edgeR.html Network Analyst Zhou et al., 2019a34 https://www.networkanalyst.ca/ NetworkAnalyst/home.xhtml Morpheus Broad Institute, Cambridge, MA https://software.broadinstitute.org/ morpheus Uwot McInnes, Healy and Melville, 201873 https://github.com/jlmelville/uwot ClusterProfiler Yu et al., 201274 https://guangchuangyu.github.io/software/ clusterProfiler/ Metacycle Wu et al., 201643 https://github.com/gangwug/MetaCycle Metascape Zhou et al., 2019b75 https://metascape.org/gp/index.html#/ main/step1 WebGestaltR v0.3.1 Liao et al., 201976 http://www.webgestalt.org/ PSEA Zhang et al., 201647 https://github.com/ranafi/PSEA (Continued on next page) e1 Cell Metabolism 35, 150–165.e1–e4, January 3, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER g:Profiler Raudvere et al., 201977 https://biit.cs.ut.ee/gprofiler/gost Metaboanalyst v5.0 Pang et al., 202151 https://www.metaboanalyst.ca/ MetaboAnalyst/faces/home.xhtml Other Rodent Diet With 45 kcal% Fat Research Diets, Inc. D12451 Rodent regular chow diet LabDiet 5053 - PicoLab Rodent diet 20 extruded, #3002890-712
RNA Sequencing:Article Title: Diurnal transcriptome landscape of a multi-tissue response to time-restricted feeding in mammals.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Infinity Cholesterol assay kit Thermo Scientific #TR13421 Infinity Triglycerides assay kit Thermo Scientific #TR22421 Mouse Insulin ELISA kit Crystal Chem #90080 Mouse Leptin ELISA kit Crystal Chem #90030 Autokit 3-HB kit Wako Diagnostics #417-73501 Quant-iT RNA Assay Kit Thermo Scientific #Q33140 Quant-iT DNA Assay Kit Thermo Scientific #Q33120 TruSeq Stranded mRNA kit Illumina #20020595 Deposited data Raw files for RNA sequencing This paper GSE190389 TMM normalized counts, statistical analyses for differential and rhythmic gene expression, and liver metabolome counts and statistical analyses This paper https://data.mendeley.com/datasets/ wc5wy48x93/draft?a=8aafd31c-bdf94782-bffe-10eccb3dd093 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory #000664 Software and algorithms Prism 6.0 GraphPad Software https://www.graphpad.com R, v4.0.3 R Development Core Team, 2022 https://www.R-project.org/ Rstudio, v1.3.1093 Rstudio: Integrated Development for R, Boston, MA https://www.rstudio.com/ FastQC, v0.11.5 Babraham Bioinformatics, Cambridge, UK https://www.bioinformatics.babraham.ac. uk/projects/fastqc/ STAR v2.5.3a Dobin et al., 201369 https://github.com/alexdobin/STAR HOMER v4.10 Heinz et al., 201070 http://homer.ucsd.edu/homer/ DESeq2 v1.24.0 Love, Huber and Anders, 201471 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html edgeR v3.26.7 Robinson, McCarthy and Smyth, 2010;33 McCarthy, Chen and Smyth, 201272 https://bioconductor.org/packages/ release/bioc/html/edgeR.html Network Analyst Zhou et al., 2019a34 https://www.networkanalyst.ca/ NetworkAnalyst/home.xhtml Morpheus Broad Institute, Cambridge, MA https://software.broadinstitute.org/ morpheus Uwot McInnes, Healy and Melville, 201873 https://github.com/jlmelville/uwot ClusterProfiler Yu et al., 201274 https://guangchuangyu.github.io/software/ clusterProfiler/ Metacycle Wu et al., 201643 https://github.com/gangwug/MetaCycle Metascape Zhou et al., 2019b75 https://metascape.org/gp/index.html#/ main/step1 WebGestaltR v0.3.1 Liao et al., 201976 http://www.webgestalt.org/ PSEA Zhang et al., 201647 https://github.com/ranafi/PSEA (Continued on next page) e1 Cell Metabolism 35, 150–165.e1–e4, January 3, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER g:Profiler Raudvere et al., 201977 https://biit.cs.ut.ee/gprofiler/gost Metaboanalyst v5.0 Pang et al., 202151 https://www.metaboanalyst.ca/ MetaboAnalyst/faces/home.xhtml Other Rodent Diet With 45 kcal% Fat Research Diets, Inc. D12451 Rodent regular chow diet LabDiet 5053 - PicoLab Rodent diet 20 extruded, #3002890-712
Gene Expression:Article Title: Diurnal transcriptome landscape of a multi-tissue response to time-restricted feeding in mammals.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Infinity Cholesterol assay kit Thermo Scientific #TR13421 Infinity Triglycerides assay kit Thermo Scientific #TR22421 Mouse Insulin ELISA kit Crystal Chem #90080 Mouse Leptin ELISA kit Crystal Chem #90030 Autokit 3-HB kit Wako Diagnostics #417-73501 Quant-iT RNA Assay Kit Thermo Scientific #Q33140 Quant-iT DNA Assay Kit Thermo Scientific #Q33120 TruSeq Stranded mRNA kit Illumina #20020595 Deposited data Raw files for RNA sequencing This paper GSE190389 TMM normalized counts, statistical analyses for differential and rhythmic gene expression, and liver metabolome counts and statistical analyses This paper https://data.mendeley.com/datasets/ wc5wy48x93/draft?a=8aafd31c-bdf94782-bffe-10eccb3dd093 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory #000664 Software and algorithms Prism 6.0 GraphPad Software https://www.graphpad.com R, v4.0.3 R Development Core Team, 2022 https://www.R-project.org/ Rstudio, v1.3.1093 Rstudio: Integrated Development for R, Boston, MA https://www.rstudio.com/ FastQC, v0.11.5 Babraham Bioinformatics, Cambridge, UK https://www.bioinformatics.babraham.ac. uk/projects/fastqc/ STAR v2.5.3a Dobin et al., 201369 https://github.com/alexdobin/STAR HOMER v4.10 Heinz et al., 201070 http://homer.ucsd.edu/homer/ DESeq2 v1.24.0 Love, Huber and Anders, 201471 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html edgeR v3.26.7 Robinson, McCarthy and Smyth, 2010;33 McCarthy, Chen and Smyth, 201272 https://bioconductor.org/packages/ release/bioc/html/edgeR.html Network Analyst Zhou et al., 2019a34 https://www.networkanalyst.ca/ NetworkAnalyst/home.xhtml Morpheus Broad Institute, Cambridge, MA https://software.broadinstitute.org/ morpheus Uwot McInnes, Healy and Melville, 201873 https://github.com/jlmelville/uwot ClusterProfiler Yu et al., 201274 https://guangchuangyu.github.io/software/ clusterProfiler/ Metacycle Wu et al., 201643 https://github.com/gangwug/MetaCycle Metascape Zhou et al., 2019b75 https://metascape.org/gp/index.html#/ main/step1 WebGestaltR v0.3.1 Liao et al., 201976 http://www.webgestalt.org/ PSEA Zhang et al., 201647 https://github.com/ranafi/PSEA (Continued on next page) e1 Cell Metabolism 35, 150–165.e1–e4, January 3, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER g:Profiler Raudvere et al., 201977 https://biit.cs.ut.ee/gprofiler/gost Metaboanalyst v5.0 Pang et al., 202151 https://www.metaboanalyst.ca/ MetaboAnalyst/faces/home.xhtml Other Rodent Diet With 45 kcal% Fat Research Diets, Inc. D12451 Rodent regular chow diet LabDiet 5053 - PicoLab Rodent diet 20 extruded, #3002890-712
Software:Article Title: Diurnal transcriptome landscape of a multi-tissue response to time-restricted feeding in mammals.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays Infinity Cholesterol assay kit Thermo Scientific #TR13421 Infinity Triglycerides assay kit Thermo Scientific #TR22421 Mouse Insulin ELISA kit Crystal Chem #90080 Mouse Leptin ELISA kit Crystal Chem #90030 Autokit 3-HB kit Wako Diagnostics #417-73501 Quant-iT RNA Assay Kit Thermo Scientific #Q33140 Quant-iT DNA Assay Kit Thermo Scientific #Q33120 TruSeq Stranded mRNA kit Illumina #20020595 Deposited data Raw files for RNA sequencing This paper GSE190389 TMM normalized counts, statistical analyses for differential and rhythmic gene expression, and liver metabolome counts and statistical analyses This paper https://data.mendeley.com/datasets/ wc5wy48x93/draft?a=8aafd31c-bdf94782-bffe-10eccb3dd093 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory #000664 Software and algorithms Prism 6.0 GraphPad Software https://www.graphpad.com R, v4.0.3 R Development Core Team, 2022 https://www.R-project.org/ Rstudio, v1.3.1093 Rstudio: Integrated Development for R, Boston, MA https://www.rstudio.com/ FastQC, v0.11.5 Babraham Bioinformatics, Cambridge, UK https://www.bioinformatics.babraham.ac. uk/projects/fastqc/ STAR v2.5.3a Dobin et al., 201369 https://github.com/alexdobin/STAR HOMER v4.10 Heinz et al., 201070 http://homer.ucsd.edu/homer/ DESeq2 v1.24.0 Love, Huber and Anders, 201471 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html edgeR v3.26.7 Robinson, McCarthy and Smyth, 2010;33 McCarthy, Chen and Smyth, 201272 https://bioconductor.org/packages/ release/bioc/html/edgeR.html Network Analyst Zhou et al., 2019a34 https://www.networkanalyst.ca/ NetworkAnalyst/home.xhtml Morpheus Broad Institute, Cambridge, MA https://software.broadinstitute.org/ morpheus Uwot McInnes, Healy and Melville, 201873 https://github.com/jlmelville/uwot ClusterProfiler Yu et al., 201274 https://guangchuangyu.github.io/software/ clusterProfiler/ Metacycle Wu et al., 201643 https://github.com/gangwug/MetaCycle Metascape Zhou et al., 2019b75 https://metascape.org/gp/index.html#/ main/step1 WebGestaltR v0.3.1 Liao et al., 201976 http://www.webgestalt.org/ PSEA Zhang et al., 201647 https://github.com/ranafi/PSEA (Continued on next page) e1 Cell Metabolism 35, 150–165.e1–e4, January 3, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER g:Profiler Raudvere et al., 201977 https://biit.cs.ut.ee/gprofiler/gost Metaboanalyst v5.0 Pang et al., 202151 https://www.metaboanalyst.ca/ MetaboAnalyst/faces/home.xhtml Other Rodent Diet With 45 kcal% Fat Research Diets, Inc. D12451 Rodent regular chow diet LabDiet 5053 - PicoLab Rodent diet 20 extruded, #3002890-712
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