Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMARCA4

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
Brg1_EtOH_ChIPseq
cell line/type
A1-2 breast cancer cells
treatment
1hr EtOH
chip antibody
lab-made rabbit anti-Brg1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, cells were fixed with 1% formaldehyde at 37C for 10 minutes for all targets except BRG1, for which cells were fixed for 20 minutes. After quenching with glycine, cell pellets were washed Hypotonic buffer (10mM HEPES-NaOH pH 7.9, 10 mM KCl, 1.5 mM MgCl2, 340 mM sucrose, 10% glycerol, 0.1% Triton X-100, and HALT protease inhibitors (ThermoFisher)) and resuspended in Shearing buffer (10 mM Tris-HCl pH 8.0, 1mM EDTA, 0.5mM EGTA, 0.5mM PMSF, 5mM Sodium Butyrate, 0.1% SDS, and HALT protease inhibitors (ThermoFisher) and chromatin was fragmented by sonication with the Covaris S220. Chromatin was diluted two-fold in 2xIP buffer (20 mM Tris-HCl pH 8.0, 300mM NaCl, 2mM EDTA, 20% Glycerol, 1% Triton X-100, 0.5mM PMSF, 5mM Sodium Butyrate, and HALT protease inhibitors (ThermoFisher)) and immunoprecipitation was performed with 1ug antibody per 100ug chromatin. Immune complexes were captured using protein A and G dynabeads, washed once each with low salt (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1 % Triton X-100, 0.1 % SDS), high salt (same as low salt buffer, except 500 mM NaCl), and LiCl buffer (Tris-HCl pH 8.0, 250 mM LiCl, 2 mM EDTA, 1 % NP-40, 1 % (wt/vol) sodium deoxycholate), and twice with TE. Eluted DNA was RNaseA and Proteinase K treated and purified using Qiagen PCR purification columns. For RNA-seq, RNA was isolated from treated A1-2 and A1A3 cells using Qiagen RNeasy kits with on-column DNase treatment. ChIP-seq libraries were generated using the Illumina Nextara-XT library generation kit, RNA-seq libraries were generated at the National Intramural Sequencing Center using Ribo-Zero Gold

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
63276275
Reads aligned (%)
131.7
Duplicates removed (%)
19.1
Number of peaks
855 (qval < 1E-05)

hg38

Number of total reads
63276275
Reads aligned (%)
134.3
Duplicates removed (%)
18.3
Number of peaks
1055 (qval < 1E-05)

Base call quality data from DBCLS SRA