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 |