Identifying multiscale translational safety biomarkers using a network-based systems approach

. 2023 Jan 31;26(3):106094. doi: 10.1016/j.isci.2023.106094

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies

Mouse monoclonal anti-MTHFD2	ABCAM	4G7-2G3; RRID: AB_2147537
Rabbit monoclonal anti-TRIB3	ABCAM	EPR3151Y; RRID: AB_1267365
Mouse monoclonal anti-Tubulin A	Sigma	DM 1A; RRID: AB_261775

Chemicals, peptides, and recombinant proteins

Acetamide	Sigma	CAT#A0500-1G
Acetamidofluorene	Sigma	CAT#A7015-5G
Aflatoxine B1	Sigma	CAT#A6636
Cimetidine	Sigma	CAT#C4522-5G
Colchicine	Sigma	CAT#C9754
Dexamethasone	Sigma	CAT#D4902
Diclofenac	Sigma	CAT#D6899
Diethyl maleate	Sigma	CAT#D97703
Ethambutol	Sigma	CAT#E4630-25G
Ethionamide	Sigma	CAT#E6005-5G
Famotidine	Merck	CAT#F6889-500MG
Gefitinib	Sigma	CAT#SML1657
Methapyrilene	Supelco	CAT#442641
Nefazodone	Sigma	CAT#N5536
N-Nitrosomorpholine	Sigma	CAT#N7382-1ML
Omeprazole	Supelco	CAT#PHR1059
Phorone	Sigma	CAT#MAN424067694-10G
Simvastatin	Supelco	CAT#PHR1438-1G
Tert-Butylhydroquinone	Sigma	CAT#112941
Tharpsigargin	Sigma	CAT#T9033
Ticlopidine	Sigma	CAT#T6654
Triamterene	Merck	CAT#T4143-10G
Tunicamycin C	Sigma	CAT#T7765
WY-14643	Sigma	CAT#C7081
DMSO	Sigma	CAT#D2650

Critical commercial assays

TempO-Seq	BioClavis J. M. Yeakley et al.³⁸	https://www.bioclavis.co.uk/overview
Rneasy kit	Qiagen	CAT#74004
RevertAid H Minus First strand cDNA Synthesis Kit	Thermo Scientific	CAT#K1682
PowerUp SYBR Green Master Mix	Sigma	CAT#KCQS02

Experimental models: Cell lines

HepG2 cell line	ATCC	Clone HB8065

Oligonucleotides

siRNA siGENOME MTHFD2 SMARTpool	GE Dharmacon	gene ID 10797
siRNA siGENOME TRIB3 SMARTpool	GE Dharmacon	gene ID 57761
siRNA siGENOME ATF4 SMARTpool	GE Dharmacon	gene ID 468
siRNA siGENOME DDIT3 SMARTpool	GE Dharmacon	gene ID 1649
Primer real time quantitative PCR are in suppl. Table SZ	This paper	N/A

Recombinant DNA

Bacterial Artificial Chromosomes MTHFD2	BACPAC Genomics (Emeryville, California, USA)	RP11-101L15
Bacterial Artificial Chromosomes TRIB3	BACPAC Genomics (Emeryville, California, USA)	RP11-99E14

Software and algorithms

affy R package version 1.52.0	L. Gautier et al.³⁸	http://bioconductor.org/packages/release/bioc/html/affy.html
BrainArray chip description file (CDF) version 19 Rat2302	MicroArray Lab	http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp
BrainArray chip description file (CDF) version 19 PHH	MicroArray Lab G. Callegaro et al.¹⁶	http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp
limma R package version 3.30.13	M. E. Ritchie et al.³⁹	https://bioconductor.org/packages/release/bioc/html/limma.html
DESeq2 R package version 1.28.1	M. I. Love et al.⁴⁰	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
WGCNA R package version 1.51	P. Langfelder et al.⁹	https://www.rdocumentation.org/packages/WGCNA/versions/1.51
OverRepresentation Analysis (ORA) via Consensus Pathway DB (cpdb version 34)	A. Kamburov et al.⁴¹	http://cpdb.molgen.mpg.de/CPDB
topGO R package version 2.26.0	A. Alexa et al.⁴²	https://bioconductor.org/packages/release/bioc/html/topGO.html
stat R package (R version 3.5.1)	R Core Team	https://cran.r-project.org/bin/windows/base/old/3.5.1/
DoRothEA	L. Garcia-Alonso et al.²⁶	https://bioconductor.org/packages/release/data/experiment/html/dorothea.html
TXG-MAPr	G. Callegaro et al.¹⁸	https://txg-mapr.eu/WGCNA_liver/TGGATEs_LIVER/
DisGeNET database v7.0	J. Piñero et al.¹⁴	https://www.disgenet.org/
Human Protein Atlas	M. Uhlén et al.¹⁵	https://www.proteinatlas.org/

Other

Dulbecco’s modified Eagle’s medium	Gibco	11504496
Penicillin-Streptomycin	Gibco	15070063
PageRuler™ Plus	Thermo Scientific	26620
Deposited data
TG-GATEs dataset	Igarashi et al.¹¹	Open TG-GATEs data available at http://toxico.nibio.go.jp/english/index.html
Drug Matrix dataset, rat in vivo experiments	Ganter et al. ¹²	GEO Series: GSE57815
Rat Genome Database, orthology table	Smith et al.⁴³	http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/