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. 2022 Feb 9;2(2):100098. doi: 10.1016/j.xgen.2022.100098
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies

Anti-p300 Aabcam Cat#ab14984; RRID: AB_301550
Anti-Brg-1 Santa Cruz Biotechnology Cat#sc17796; RRID: AB_626762
Anti-Gcn5 Santa Cruz Biotechnology Cat#sc365321x; RRID: AB_10846182
Anti-RBBP5 Bethyl Laboratories Cat#A300-109A; RRID: AB_210551
Anti-TBL1XR1 Santa Cruz Biotechnology Cat#sc100908; RRID: AB_1130006
Anti-HDAC1 Abcam Cat#ab7028; RRID: AB_305705
Anti-MED1 Bethyl Laboratories Cat#A300-793A; RRID: AB_577241
Anti-BRD4 Bethyl Laboratories Cat#A301-985A50; RRID: AB_1576498
Anti-NFkB p65 Santa Cruz Biotechnology Cat#sc372; RRID: AB_632037
Anti-NFkB p65 Santa Cruz Biotechnology Cat#sc8008; RRID: AB_628017
Anti-ICSBP Santa Cruz Biotechnology Cat#sc6058x; RRID: AB_649510
Anti-IRF3 Cell Signaling Technology Cat#D83B9; RRID: AB_1904036
Anti-IRF2 Santa Cruz Biotechnology Cat#sc374327; RRID: AB_10990717
Anti-PU.1 Santa Cruz Biotechnology Cat#sc352; RRID: AB_632289
Donkey anti-Goat IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 ThermoFisher Scientific Cat#A-11055; RRID: AB_2534102
Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 ThermoFisher Scientific Cat#A-11029; RRID: AB_138404
Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 ThermoFisher Scientific Cat#A-11034; RRID: AB_2576217
Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 647 ThermoFisher Scientific Cat#A32728; RRID: AB_2633277
Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 647 ThermoFisher Scientific Cat#A32733; RRID: AB_2633282
Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, HRP ThermoFisher Scientific Cat#G-21234; RRID: AB_2536530
Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, HRP ThermoFisher Scientific Cat#G-21040; RRID: AB_2536527

Chemicals, peptides, and recombinant proteins

Lipopolysaccharides from Escherichia coli O111:B4 Sigma-Aldrich Cat#L3024
Human IFN-gamma Recombinant Protein ThermoFisher Scientific Cat#PHC4031
Protease Inhibitor Cocktail Sigma-Aldrich Cat#P8340
Phosphatase Inhibitor Cocktail A Santa Cruz Biotechnology Cat#sc45055
Phorbol 12-myristate 13-acetate Sigma-Aldrich Cat#P8139

Deposited data

RBBP5 ChIP-seq data, performed in K562 cells ENCODE ENCFF666PCE
EP300 ChIP-seq data, performed in K562 cells ENCODE ENCFF755HCK
SMARCA4 ChIP-seq data, performed in K562 cells ENCODE ENCFF267OGF
TBL1XR1 ChIP-seq data, performed in K562 cells ENCODE ENCFF868SWL
CASCADE microarray data GEO GSE148945

Experimental models: Cell lines

THP-1 ATCC Cat#TIB-202

Oligonucleotides

Protein Binding Microarray Double-stranding Primer Eurofins 5′ - CAGCAGCGCTCAAGG
AATCAAGAC - 3′

Software and algorithms

RColorBrewer, version 1.1.2 Neuwirth49 N/A
Cowplot, version 1.1.1 Wilke50 N/A
ggseqlogo R package, version 0.1 Wagih51 N/A
TOMTOM (MEME suit), version 5.0.3 Patwardhan et al.52 N/A
FASTQC, version 0.11.8 Kalita et al.53 N/A
Trim Galore, version 0.4.2 Goodwin et al.54 N/A
cutadapt, version 1.9.1 Bentley et al.55 N/A
bowtie2, version 2.3.4.1 Langmead and Salzberg56 N/A
samtools, version 1.8.0 Patwardhan et al.52 N/A
IMPUTE2, version 2.3.0 Verma et al.36 N/A
cnvPartition, version 3.2.1 Illumina Genome Studio N/A
MARIO, version 3.9.3 Verma et al.36 N/A
UpSetR Package, version 1.4.0 Conway et al.57 N/A
CASCADE R-scripts, version 1.0.0 https://github.com/Siggers-Lab/CASCADE_paper N/A
ggplot2, version 3.3.5 Wickham58 N/A