Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
JUN

Cell type

Cell type Class
Breast
Cell type
MDA-MB-231
Primary Tissue
Breast
Site of Extraction
Effusion, Pleural
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
AP1_Dexamethasone
cell line
MDA-MB-231
cancer
Breast adenocarcinoma
type
TNBC
chip antibody
c-Jun Antibody (H-79) from Santa Cruz Biotechnology

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
After treatment with 100 nM Dex, 10 uM CpdA or vehicle for 1 h, MDA-MB-231 cells were crosslinked with 1% formaldehyde for 10 min. Sonicated chromatin was enriched by immunoprecipatation with an anti-GR antibody. MDA-MB-231 cells were treated with 100 nM Dex, or 10 M CpdA for 2h and 4h, respectively. RNA was extracted using the RNeasy Mini Kit. For ChIP-exo, T4 DNA polymerase, T4 PNK, and Klenow DNA Polymerase were used together for end polishing. The ligation step was performed with less reducing agent. Protein A Dynal magnetic beads were washed using modified RIPA buffer (50mM Tris-HCL pH 7.8, 1mM EDTA, 0.25% Na Deoxycholate, 1% NP-40, 0.5M LiCl). The library was amplified with only 10 or 12 PCR cycles, and prepared without gel-based size selection. For RNA-seq, libraries were constructed using the Illumina Truseq RNA Sample Prep Kit according to the manufacturer's protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
67589596
Reads aligned (%)
63.9
Duplicates removed (%)
34.4
Number of peaks
14202 (qval < 1E-05)

hg38

Number of total reads
67589596
Reads aligned (%)
65.9
Duplicates removed (%)
33.0
Number of peaks
14377 (qval < 1E-05)

Base call quality data from DBCLS SRA