KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Chemicals, Peptides, and Recombinant Proteins | ||
| Q6 internal standard | Avanti Polar Lipids | Cat# 900150 |
| PC(15:0/15:0) internal standard | Avanti Polar Lipids | Cat# 850350P |
| PS(17:0/17:0) internal standard | Avanti Polar Lipids | Cat# 840028P |
| PE(15:0/15:0) internal standard | Avanti Polar Lipids | Cat# 850704P |
| PA(17:0/17:0) internal standard | Avanti Polar Lipids | Cat# 830856P |
| PG(15:0/15:0) internal standard | Avanti Polar Lipids | Cat# 840446P |
| CL(56:0) internal standard | Avanti Polar Lipids | Cat# 750332P |
| FA(15:0/15:0) internal standard, Pentadecanoic Acid | Sigma-Aldrich | Cat# 91446 |
| SPLASH® Lipidomix® Mass Spec Standard | 330707 | Avanti Polar Lipids | Cat# 330707 |
| Critical Commercial Assays | ||
| AST: AST Flex® reagent cartridge | Siemens Healthcare | Cat# DF41A |
| ALT: ALTI Flex® reagent cartridge | Siemens Healthcare | Cat# DF143 |
| LDL: ALDL Flex® reagent cartridge | Siemens Healthcare | Cat# DF131 |
| HDL: AHDL Flex® reagent cartridge | Siemens Healthcare | Cat# DF48B |
| Cholesterol: CHOL Flex® reagent cartridge | Siemens Healthcare | Cat# DF27 |
| Plasma TG: TGL Flex® reagent cartridge | Siemens Healthcare | Cat# DF69A |
| LDH: LDI Flex® reagent cartridge | Siemens Healthcare | Cat# DF54 |
| HR Series NEFA-HR(2) | FUJIFILM Wako Dignostics | http://www.wakodiagnostics.com/r_nefa.html |
| Glucose: GLUC Flex® reagent cartridge | Siemens Healthcare | Cat# DF40 |
| Mercodia Mouse Insulin ELISA kit | Mercodia | Cat# 10-1247-01 |
| Liver TG: Serum Triglyceride Determination Kit | Sigma-Aldrich | Cat#TR0100 |
| Deposited Data | ||
| BXD plasma lipidomics data [raw] | This paper | https://chorusproject.org/anonymous/download/experiment/1b742397d9114a27bcd63b40db2057f2 |
| BXD plasma lipidomics data [normalized] | This paper |
http://www.genenetwork.org/ GN Accession: GN602. RecordIDs 19545–19802 |
| BXD mouse genotype data | http://www.genenetwork.org/ | GN Accession: GN600 |
| BXD mouse metabolic phenotype data | http://www.genenetwork.org/ | GN Accession: GN602 |
| BXD mouse liver transcriptome data | http://www.genenetwork.org/ | GN Accession: GN432 (CD), GN431 (HFD) |
| BXD mouse Subcutaneous WAT transcriptome data | http://www.genenetwork.org/ | GN Accession: GN779 (CD), GN778 (HFD) |
| BXD mouse heart transcriptome data | http://www.genenetwork.org/ | GN Accession: GN485 (CD), GN486 (HFD) |
| BXD mouse quadriceps transcriptome data | http://www.genenetwork.org/ | GN Accession: GN379 (CD), GN380 (HFD) |
| GWASdb2 | (Li et al., 2016) | http://jjwanglab.org/gwasdb |
| GWAS Catalog | (MacArthur et al., 2017) | https://www.ebi.ac.uk/gwas/ |
| Software and Algorithms | ||
| R | The R Foundation | https://www.r-project.org/ |
| MATLAB | Mathworks | https://www.mathworks.com |
| MATLAB Bioinformatics Toolbox | Mathworks | https://www.mathworks.com/products/bioinfo.html |
| corrgram | The R Foundation | https://cran.r-project.org/web/packages/corrgram/index.html |
| R/qtl (v 1.39–5) package | (Broman et al., 2003) | http://www.rqtl.org/ |
| Unweighted correlation network | custom package imsbInfer | Github (https://github.com/wolski/imsbInfer) |
| biomaRt | Bioconductor | http://bioconductor.org/packages/biomaRt/ |
| clusterProfiler | (Yu et al., 2012) | https://bioconductor.org/packages/release/\bioc/html/clusterProfiler.html |
| LipidSearch | Thermo Scientific | https://www.thermofisher.com/order/catalog/product/IQLAAEGABSFAPCMBFK |
| GraphPad Prism 7 | GraphPad | https://www.graphpad.com/ |
| Other | ||
| Q Exactive mass spectrometer, Build 2.3 SP2 | Thermo Scientific | https://www.thermofisher.com/order/catalog/product/IQLAAEGAAPFALGMAZR |