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. Author manuscript; available in PMC: 2021 Nov 25.
Published in final edited form as: Cell. 2020 Nov 25;183(5):1185–1201.e20. doi: 10.1016/j.cell.2020.11.002

KEY RESOURCE TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Code
WGCNA code (Method S1) This paper N/A
Biological Samples
Human Blood NASA Twin Study http://www.nasa.gov/twins-study/
Human T Cells ISS Expedition 14 https://www.nasa.gov/mission_pages/station/expeditions/expedition14/
Human Hair Follicles ISS Expeditions from July 2009 to February 2013 https://www.nasa.gov/mission_pages/station/expeditions/past.html
Mouse adrenal gland NASA Rodent Research-1 Mission https://lsdajsc.nasa.gov/Experiment/exper/13380
Mouse extensor digitorum longus muscle NASA Rodent Research-1 Mission https://lsda.lsc.nasa.gov/Experiment/exper/13380
Mouse eye NASA Rodent Research-1 Mission https://lsda.isc.nasa.gov/Experiment/exper/13380
Mouse gastrocnemius muscle NASA Rodent Research-1 Mission https://lsda.jsc.nasa.gov/Experiment/exper/13380
Mouse kidney NASA Rodent Research-1 Mission https://lsda.jsc.nasa.gov/Experiment/exper/13380
Mouse Liver NASA Rodent Research-1 Mission https://lsda.jsc.nasa.gov/Experiment/exper/13380
Mouse quadriceps muscle NASA Rodent Research-1 Mission https://lsda.isc.nasa.gov/Experiment/exper/13380
Mouse soleus muscle NASA Rodent Research-1 Mission https://lsda.jsc.nasa.gov/Experiment/exper/13380
Mouse tibialis anterior muscle NASA Rodent Research-1 Mission https://lsdaisc.nasa.gov/Experiment/exper/13380
Mouse adrenal gland NASA Rodent Research-3 Mission https://lsdajsc.nasa.gov/Experiment/exper/13961
Mouse eye NASA Rodent Research-3 Mission https://lsda.jsc.nasa.gov/Experiment/exper/13961
Mouse kidney NASA Rodent Research-3 Mission https://lsda.jsc.nasa.gov/Experiment/exper/13961
Mouse Liver NASA Rodent Research-3 Mission https://lsdaisc.nasa.gov/Experiment/exper/13961
Mouse gastrocnemius muscle NASA Rodent Research-9 Mission https://lsdajsc.nasa.gov/Experiment/exper/13964
Mouse quadriceps muscle NASA Rodent Research-9 Mission https://lsdajsc.nasa.gov/Experiment/exper/13964
Chemicals. Peptides, and Recombinant Proteins
D-Pantothenic acid acid hemicalcium salt Sigma Aldrich P2250
D-Malic acid Sigma Aldrich 46940-U
a-D-Glucose Sigma Aldrich 158968-25G
D-Fructose-6-phosphate disodium salt hydrate Sigma Aldrich F3627
Citric Acid Sigma Aldrich C1857
L-Carnitine hydrochloride Sigma Aldrich C0283
L-Arginine Sigma Aldrich A5006
Tetradecanoylcamitine (myristoyl-L-carnitine) Sigma Aldrich 91582
4-Nitrobenzoic acid Sigma Aldrich 72910
Debrisoquine sulfate Sigma Aldrich D1306
Chlorpropamide Sigma Aldrich C1290
Acetaminophen Sigma Aldrich 103-90-2
Sulfaguanidine Sigma Aldrich 57-67-0
Sulfadimethoxine Sigma Aldrich 122-11-2
Val-Tyr-Val Sigma Aldrich 17355-22-5
Terfenadine Sigma Aldrich 50679-08-8
Leu-Enk acetate salt hydrate Sigma Aldrich 58822-25-6
Critical Commercial Assays
micro BCA protein assay Thermo Scientifc 23235
Deposited Data
GLDS-98 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-98/
GLDS-99 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-99/
GLDS-100 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-100/
GLDS-101 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-101/
GLDS-102 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-102/
GLDS-103 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-103/
GLDS-104 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-104/
GLDS-105 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-105/
GLDS-161 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-161/
GLDS-162 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-162/
GLDS-163 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-163/
GLDS-168 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-168/
GLDS-13 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-13/
GLDS-52 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-52/
GLDS-54 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-54/
GLDS-114 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-114/
GLDS-118 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-118/
GLDS-174 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-174/
GLDS-47 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-47/
GLDS-48 NASA/GeneLab https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-48/
GLDS-343 NASA/GeneLab https://doi.org/10.26030/h968-2m75
Experimental Models: Cell Lines
Fibroblasts AG01522 Coriell Institute https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=AG01522, RRID: CVCL_H759
HUVEC ATCC HUV-EC-C [HUVEC] (ATCC CRL-1730), RRID: CVCL_2959
HMVEC-dBL LONZA Catalog Number: CC-2543
Experimental Models: Organisms/Strains
Mouse: C57BL/6 Jackson Labs C57BL/6J (Stock No: 000664)
Mouse: BALB/c Jackson Labs BALB/c (Stock No: 000651)
Oligonucleotides
Primer. MT-RNR1: Forward - ATGCAGCTCAAAACGCTTAGC This paper N/A
Primer MT-RNR1: Reverse - GCTGGCACGAAATTGACCAA This paper N/A
Primer MT-RNR2: Forward - CCCTGTACGAAAGGACAAGAGAAAT This paper N/A
Primer MT-RNR2: Reverse - TCTTGGGTGGGTGTGGGTATAAT This paper N/A
Primer: MT-COI: Forward - CAGCAGTCCTACTTCTCCTATCTCT This paper N/A
Primer MT-C01: Reverse - GGGTCGAAGAAGGTGGTGTT This paper N/A
Primer MT-C02: Forward - GCCCTTTTCCTAACACTCACAACAA This paper N/A
Primer MT-C02: Reverse - GTAAAGGATGCGTAGGGATGGG This paper N/A
Primer MT-ND1: Forward - CCCTAAAACCCGCCACATCT This paper N/A
Primer MT-ND1: Reverse - GGCTAGAATAAATAGGAGGCCTAGGT This paper N/A
Primer: 18S rRNA: Forward - GGCCCTGTAATTGGAATGAGTC This paper N/A
Primer: 18S rRNA Reverse - CCAAGATCCAACTACGAGCTT This paper N/A
Primer GAPDH: Forward - AAGGTGAAGGTCGGAGTCAAC This paper N/A
Primer GAPDH: Reverse - GGGGTCATTGATGGCAACAATA This paper N/A
Software and Algorithms
FASTQC version 0.11.8 N/A https://www.bioinformatics.babraham.ac.uk/projects/fastqc/, RRID: SCR_014583
Trim Galore! Version 0.50 N/A https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/, RRID: SCR_011847
STAR version STAR_2.6.1a_08-27 Dobin et al., 2013 https://github.com/alexdobin/STAR, RRID: SCR_015899
mice genome version mm 10-GRCm38 N/A https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.20/
RSEM version 1.3.1 Dobin et al., 2013 https://deweylab.github.io/RSEM/, RRID: SCR_013027
R Version 3.5.1 and 4.0.2 R Core Team (2020). https://www.r-project.org/, RRID: SCR_001905
DESeq2 Version 1.22.2 Love et al., 2014 https://github.com/mlkelove/DESeq2, RRID: SCR_01568
Picard MarkDuplicates v2.10.10-SNAPSHOT N/A https://broadinstitute.grthub.io/picard/, RRID: SCR_00652
MethylDackel mbias N/A https://github.com/dpryan79/MethylDackel
methylKit Akalin et al., 2012 https://www.bioconductor.org/packages/release/bioc/html/methylKit.html, RRID: SCR_005177
LIMMA Ritchie et al., 2015 https://www.bioconductor.org/packages/release/bioc/html/limma.html, RRID: SCR_010943
GSEA Sergushichev, 2016; Subramanian et al., 2005 https://www.gsea-msigdb.arg/gsea/lindex.jsp, RRID: SCR_003199
MaxQuant (1.6.2.3) Tyanova et al., 2016a https://www.maxquarst.org/, RRID: SCR_014485
Uniprot (downloaded on 20180104) Tyanova et al., 2016a https://www.unipfot.org/, RRID: SCR_002380
PTXQC Bielow et al., 2016 https://github.com/cbielow/PTXQC
Perseus (1.6.2.2) Tyanova et al., 2016b https://maxquant.net/perseus/, RRID: SCR_015753
NCI DAVID Huang et al., 2009 https://david.ncifcrf.gov/, RRID: SCR_00188
EnhancedVolcano package (Bioconductor) Ritchie et al., 2015 http://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html, RRID: SCR_018931
Cytoscape Shannon et al., 2003 https://cytoscape.org, RRID: SCR_003032
ClueGo Bindea et al., 2009 http://apps.cytoscape.org/apps/cluego, RRID: SCR_005748
EnrichmentMap Merico et al., 2010 http://apps.cytoscape.org/apps/enrichmentmap, RRID: SCR_016052
Progenesis QI N/A http://www.nonlinear.com/progenesis/qi/, RRID: SCR_018923
MetaboLyzer Mak et al., 2014 https://sites.google.com/a/georgetown.edu/fornace-lab-informatics/home/metabotyzer
Gene Expression Dynamics Inspector (GEDI) Eichler et al., 2003 RRID: SCR_008530
MetaboAnalyst Chong et al., 2018 https://www.metaboanatyst.ca/, RRID: SCR_015539
Python version 3.7.6 and version 3.8.3 Van Rossum and Drake, 1995 https://www.python.org/downloads/release/python-376/
https://www.python.org/downloads/release/python-383/, RRID: SCR_008394
COBRApy version 0.19.0 (using Python 3.8.3) Ebrahim et al., 2013 https://pypi.org/project/cobra/, RRID: SCR_01209
Corda version 0.4.2 (for COBRApy) Schultz and Qutub, 2016 https://github.com/qutubiab/CORDA
imm1415 metabolic model from BiGG (for COBRApy) Sigurdsson et al., 2010 https://www.ebi.ac.uk/biomodels/MODEL1507180055
Gurobi Optimizer version 8.1.0 LP (for COBRApy) Gurobi Optimization. L. L. C. (2020). https://www.gurobi.com/
Numpy python package v 1.18.1 (with Python 3.7.6) Harris et al., 2020 https://njmpy.org/, RRID: SCR_008633
Escher version 1.7.3 (with Python 3.7.6) King et al., 2015 http://escher.github.io/#/
pandas 1.0.1 (with Python 3.7.6) N/A https://pancas.pydata.org/, RRID: SCR_018214
ipython version 7.12.0 (with Python 3.7.6) Perez and Granger, 2007 https://ipython.org/, RRID: SCR_001658
Jupyter Notebook 6.0.3 (with Python 3.7.6) Kluyver et al., (2016). https://jupyter.org/, RRID: SCR_018315
pheatmap R package version 1.0.12 Kolde (2015). https://github.com/raivokolde/pheatmap, RRID: SCR_016418
bwa-meth version 0.2.2 Pedersen et al., 2014 https://github.com/brentp/bwa-meth
Kallisto Bray et al., 2016 https://pachterlab.github.io/kallito/, RRID: SCR_016582
Other
GeneLab NASA https://genelab.nasa.gov/