KEY RESOURCES TABLE
| 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 | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=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-bdf9-4782-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., 2013 | https://github.com/alexdobin/STAR |
| HOMER v4.10 | Heinz et al., 2010 | http://homer.ucsd.edu/homer/ |
| DESeq2 v1.24.0 | Love, Huber and Anders, 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| edgeR v3.26.7 | Robinson, McCarthy and Smyth, 2010; McCarthy, Chen and Smyth, 2012 | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| Network Analyst | Zhou et al., 2019a | https://www.networkanalyst.ca/NetworkAnalyst/home.xhtml |
| Morpheus | Broad Institute, Cambridge, MA | https://software.broadinstitute.org/morpheus |
| uwot | McInnes, Healy and Melville, 2018 | https://github.com/jlmelville/uwot |
| ClusterProfiler | Yu et al., 2012 | https://guangchuangyu.github.io/software/clusterProfiler/ |
| Metacycle | Wu et al., 2016 | https://github.com/gangwug/MetaCycle |
| Metascape | Zhou et al., 2019b | https://metascape.org/gp/index.html#/main/step1 |
| WebGestaltR v0.3.1 | Liao et al., 2019 | http://www.webgestalt.org/ |
| PSEA | Zhang et al., 2016 | https://github.com/ranafi/PSEA |
| g:Profiler | Raudvere et al., 2019 | https://biit.cs.ut.ee/gprofiler/gost |
| Metaboanalyst v5.0 | Pang et al., 2021 | 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 |