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. 2024 Aug 6;4(9):100628. doi: 10.1016/j.xgen.2024.100628
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Human CD4+ T cell Isolation Kit Miltenyi Biotec Cat#130-096-533; RRID: AB_2916089
Human Monocyte Isolation Kit Miltenyi Biotec Cat#130-091-153
T cell Activation/Expansion kit, human Miltenyi Biotect Cat#130-091-441
Biological Samples
Primary CD4+ T cells This paper N/A
Primary Monocytes This paper N/A
Chemicals, Peptides, and Recombinant Proteins
Sodium heparin tubes BD Vacutainer GTIN:00382903678747
FBS Hyclone Cat#SH30071
DMSO Sigma-Aldrich Cat#D8418
Trizol Reagent Life Technologies Cat#15596026
Chloroform Millipore Sigma Cat#CX1055-6
Acid Phenol:Chloroform Life Technologies Cat#AM9722
Glycoblue Life Technologies Cat#AM9515
Sodium acetate Invitrogen Cat#AM9740
RNase-free ethanol PharmCo Cat#111000200
RNase-free water Ambion Cat#AM9937
RPMI Medium 1640 Gibco Life Tech Cat#31800-089
AB Serum Valley Biomedical Cat#HP1022HI
IL-2 Corning Cat#356043
Critical Commercial Assays
Qubit RNA HS Assay Kit ThermoFisher Cat#Q32855
Fragment Analyzer RNA Kit Agilent Cat#DNF-471
KAPA mRNA HyperPrep Kit Roche Cat#KK8581
PippinHT 2% Agarose Gel Cassettes Sage Science Cat#HTC2010
Quick RNA Microprep kit Zymo Cat#R1050
xGen RNA Library Preparation kit IDT Cat#10009814
Deposited Data
Raw, de-identified RNA-Seq data This paper dbGaP: phs002481
Processed data This paper https://doi.org/10.5281/zenodo.11889919
Custom GENCODE v24 transcriptome annotation Godfrey et al.55 https://doi.org/10.5281/zenodo.3627233
RNA-Seq LCLs San Roman et al.11; San Roman et al.12 dbGaP: phs002481
RNA-Seq Fibroblasts San Roman et al.11; San Roman et al.12 dbGaP: phs002481
Molecular Signatures Database (MSigDB) v2022.1.Hs Subramanian et al.42; Liberzon et al.56 https://www.gseamsigdb.org/gsea/msigdb/
ZFX ChIP-seq HCT116 ENCODE ENCFF858YWR, ENCFF102UZB
ZFX ChIP-seq C4-2B ENCODE ENCFF160AXQ, ENCFF264NUJ
ZFX- ChIP-seq MCF-7 ENCODE ENCFF861DOL, ENCFF429AXS
ZFX ChIP-Seq HEK-293T ENCODE ENCFF292HYE, ENCFF625XHP
RNA-seq HCT-116 ENCODE ENCFF435PHM
RNA-Seq C4-2B Rhie et al.37 GSE102616
RNA-Seq MCF-7 ENCODE ENCFF721BRA
RNA-Seq MCF-7 Rhie et al.37 GSE102616
RNA-Seq HEK-293T Ni et al.38 GSE145160
Allelic expression data in fibroblasts and hybrid cell lines Carrel et al.33 N/A
Allelic expression data in LCLs and fibroblasts from paired genomic and cDNA SNP-chips Cotton et al.34 N/A
Allelic expression data from bulk and single LCLs in GTEx Tukiainen et al.27 N/A
Allelic expression data in single fibroblasts Garieri et al.35 N/A
Allelic expression data in bulk LCLs Sauteraud et al.36 N/A
Software and Algorithms
R v3.6.3 The R Foundation https://www.rproject.org
kallisto v0.42.5 Bray et al.57 https://pachterlab.github.io/kallisto/
tximport v1.30.0 Soneson et al.58 https://bioconductor.org/packages/release/bioc/html/tximport.html
DESeq2 v1.26.0 Love et al.59 https://bioconductor.org/packages/release/bi oc/html/DESeq2.html
BEDTools v2.26.0 Quinlan et al.60 https://bedtools.readthedocs.io/
fgsea v1.28.0 Korotkevich et al.61 https://bioconductor.org/packages/release/bioc/html/fgsea.html
Other
5Prime Gel Heavy PhaseLock tubes Quantabio Cat#2302830
Thermomixer Eppendorf N/A
Qubit 4 Fluorometer ThermoFisher N/A
5200 Fragment Analyzer System Agilent N/A
PippinHT System Sage Sciences N/A
HiSeq 2500 Illumina N/A
Cell Countess II ThermoFisher N/A