Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMARCA4

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
Sample_DMSO_CR_KO_BRG1
cell line
MCF-7
cell line
Breast Cancer Cells
genotype
ARID1A KO
sgguide
sgARID1A-2
chip-antibody
BRG1-2 (Abcam, ab110641)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The fixed cells were lysed in SDS buffer and the chromatin was sheared by Covaris sonication. The sheared chromatin was incubated with the aforementioned antibodies and protein G-Dynabeads. The samples underwent decrosslinking, RNase and proteinase K treatment. DNA fragments were eluted using AMP Pure beads, library was prepared and samples were subjected to high-throughput sequencing using HiSeq 2000 platform (Illumina). 

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
28524127
Reads aligned (%)
90.7
Duplicates removed (%)
6.5
Number of peaks
3113 (qval < 1E-05)

hg38

Number of total reads
28524127
Reads aligned (%)
92.4
Duplicates removed (%)
5.4
Number of peaks
3055 (qval < 1E-05)

Base call quality data from DBCLS SRA