Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMARCA4

Cell type

Cell type Class
Breast
Cell type
T-47D
Primary Tissue
Breast
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by original data submitter

Sample

source_name
Breast cancer cells
cell line
T47D
small interfering knock-down
none
time after r5020
0 hours
chip antibody
anti_BRG1 Abcam ab110641 [EPNCIR111A]

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq and Mnase-seq experiments were performed according to Vicent et al., Methods Mol Biol. 2014;1204:1-14. Book “Steroid receptors: Methods and protocols”, Humana press (Springer, U.S.A.) Progesterone receptor interaction with chromatin We have used the NEBNext Ultra DNA Library Prep kit for Illumina (Ref.:#7370), with amplification by Real Time PCR (light cycler) to determine the optimal number of cycles to amplify the library

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
102628445
Reads aligned (%)
58.4
Duplicates removed (%)
40.2
Number of peaks
1444 (qval < 1E-05)

hg38

Number of total reads
102628445
Reads aligned (%)
60.7
Duplicates removed (%)
38.5
Number of peaks
1359 (qval < 1E-05)

Base call quality data from DBCLS SRA