Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ARID2

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
MCF7-ARID1A KO Clone 11_ARID2 ChIP-seq_4-hydroxytamoxifen
cell line
MCF7
cell type
ER+ Breast Cancer Cell Line
passages
35-45
treatment
100 nM 4-hydroxy tamoxifen for 6 hours
chip antibody
Bethyl A302-229A

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclear lysates were prepared and antibody-bound chromatin was purified using appropriate antibodies. Antibodies used: ARID1A HPA005456, BRG1 ab215998, SNF5 Bethyl A301-087A, ERα ab3575 and Merck Millipore 06-935 antibody mix, H3K27ac Diagenode C15410196 Premium, HDAC1 Diagenode Premium C15410325, ARID2 Bethyl A302-229A, BRD4 from Cheng Ming Chiang's lab. DNA was prepared for Illumina sequencing on the HiSeq 4000 using the ThruPLEX DNA-seq kit according to the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg19

Number of total reads
40038367
Reads aligned (%)
84.6
Duplicates removed (%)
13.8
Number of peaks
1374 (qval < 1E-05)

hg38

Number of total reads
40038367
Reads aligned (%)
86.7
Duplicates removed (%)
12.5
Number of peaks
1149 (qval < 1E-05)

Base call quality data from DBCLS SRA