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. 2021 Aug 31;1(1):100003. doi: 10.1016/j.xgen.2021.100003
REAGENT or RESOURCE SOURCE IDENTIFIER
Chemicals, peptides, and recombinant proteins
Pierce Protease Inhibitor Tablets Thermo Fisher A32963
Pierce Phosphatase Inhibitor Mini Tablets Thermo Fisher A32957
Trypsin Protease MS grade, Frozen Thermo Fisher 90305R200
Lys-C, Mass Spectrometry Grade Wako Chemicals Barcode#4987481427648
TMT10plex Isobaric Label reagent Set plus TMT11-131C Label Reagent Thermo Fisher A34808
Critical commercial assays
Pierce BCA Protein Assay Kit Thermo Fisher 23227
Deposited data
CC liver proteomics ProteomeXchange (http://www.proteomexchange.org) PXD018886
DO and founder strain liver proteomics Chick et al.1; ProteomeXchange (http://www.proteomexchange.org) PXD002801
Processed data (e.g., proteins, peptides, genotypes) and code to generate all results and figures https://doi.org/10.6084/m9.figshare.12818717 N/A
CC liver proteomics QTL Viewer https://qtlviewer.jax.org/viewer/FerrisCC N/A
DO liver proteomics QTL Viewer https://qtlviewer.jax.org/viewer/SvensonHFD N/A
Experimental models: Organisms/strains
Mouse: A/J The Jackson Laboratory JAX: 000646
Mouse: C57BL/6J The Jackson Laboratory JAX: 000664
Mouse: 129S1/SvImJ The Jackson Laboratory JAX: 002448
Mouse: NOD/ShiLtJ The Jackson Laboratory JAX: 001976
Mouse: NZO/HlLtJ The Jackson Laboratory JAX: 002105
Mouse: CAST/EiJ The Jackson Laboratory JAX: 000928
Mouse: PWK/PhJ The Jackson Laboratory JAX: 003715
Mouse: WSB/EiJ The Jackson Laboratory JAX: 001145
Mouse: J:DO The Jackson Laboratory JAX: 009376
Mouse: CC001/Unc UNC Systems Genetics Core N/A
Mouse: CC002/Unc UNC Systems Genetics Core N/A
Mouse: CC003/Unc UNC Systems Genetics Core N/A
Mouse: CC004/TauUnc UNC Systems Genetics Core N/A
Mouse: CC005/TauUnc UNC Systems Genetics Core N/A
Mouse: CC006/TauUnc UNC Systems Genetics Core N/A
Mouse: CC007/Unc UNC Systems Genetics Core N/A
Mouse: CC008/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC009/UncJ UNC Systems Genetics Core N/A
Mouse: CC010/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC011/Unc UNC Systems Genetics Core N/A
Mouse: CC012/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC013/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC015/Unc UNC Systems Genetics Core N/A
Mouse: CC016/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC019/TauUnc UNC Systems Genetics Core N/A
Mouse: CC021/Unc UNC Systems Genetics Core N/A
Mouse: CC023/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC024/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC025/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC026/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC027/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC029/Unc UNC Systems Genetics Core N/A
Mouse: CC030/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC031/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC032/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC033/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC035/Unc UNC Systems Genetics Core N/A
Mouse: CC036/Unc UNC Systems Genetics Core N/A
Mouse: CC037/TauUnc UNC Systems Genetics Core N/A
Mouse: CC038/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC039/Unc UNC Systems Genetics Core N/A
Mouse: CC040/TauUnc UNC Systems Genetics Core N/A
Mouse: CC041/TauUnc UNC Systems Genetics Core N/A
Mouse: CC042/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC043/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC044/Unc UNC Systems Genetics Core N/A
Mouse: CC045/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC046/Unc UNC Systems Genetics Core N/A
Mouse: CC049/TauUnc UNC Systems Genetics Core N/A
Mouse: CC051/TauUnc UNC Systems Genetics Core N/A
Mouse: CC053/Unc UNC Systems Genetics Core N/A
Mouse: CC055/TauUnc UNC Systems Genetics Core N/A
Mouse: CC057/Unc UNC Systems Genetics Core N/A
Mouse: CC058/Unc UNC Systems Genetics Core N/A
Mouse: CC059/TauUnc UNC Systems Genetics Core N/A
Mouse: CC060/Unc UNC Systems Genetics Core N/A
Mouse: CC061/GeniUnc UNC Systems Genetics Core N/A
Mouse: CC062/Unc UNC Systems Genetics Core N/A
Mouse: CC071/TauUnc UNC Systems Genetics Core N/A
Mouse: CC072/TauUnc UNC Systems Genetics Core N/A
Mouse: CC075/Unc UNC Systems Genetics Core N/A
Mouse: CC078/TauUnc UNC Systems Genetics Core N/A
Mouse: CC079/TauUnc UNC Systems Genetics Core N/A
Mouse: CC080/TauUnc UNC Systems Genetics Core N/A
Mouse: CC081/Unc UNC Systems Genetics Core N/A
Mouse: CC082/Unc UNC Systems Genetics Core N/A
Software and algorithms
Bioconductor Bioconductor https://bioconductor.org; RRID: SCR_006442
clusterProfiler Yu et al.63 https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html; RRID: SCR_016884
ensimplR https://github.com/churchill-lab/ensimplR N/A
evd https://cran.r-project.org/web/packages/evd N/A
intermediate https://github.com/churchill-lab/intermediate N/A
intermediate2 https://github.com/duytpm16/intermediate2 N/A
lme4 Bates et al.64 https://cran.r-project.org/web/packages/lme4/index.html; RRID: SCR_015654
pcaMethods Stacklies et al.51 https://www.bioconductor.org/packages/release/bioc/html/pcaMethods.html
QTL Viewer webtool https://github.com/churchill-lab/qtlapi N/A
R The R Project https://www.r-project.org; RRID: SCR_001905
R/qtl2 Broman et al.65 https://github.com/rqtl/qtl2; RRID: SCR_018181
Other
Complex Database Ori et al.49 http://doi.org/10.1186/s13059-016-0912-5; Table S6
DO founder haplotype dosages (genoprobs) Chick et al.1 http://doi.org/10.1038/nature18270
SQLite CC founder variant database https://doi.org/10.6084/m9.figshare.5280229.v3 N/A
Waters 100mg Sep-Pak Waters WAT036820
Orbitrap Fusion Thermo Fisher N/A
Orbitrap Fusion Lumos Thermo Fisher N/A