Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RELA

Cell type

Cell type Class
Breast
Cell type
HMEC
Primary Tissue
Breast
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
Human mammary epithelial cells (HMEC)
treatment
100 ng/mL EGF for 1 h
shRNA
none
chip antibody
anti-p65 (sc-372/C-20X)
cell type
HMEC

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq: Cells were crosslinked with 2 mM disuccinimidyl glutarate (DSG) for 45 min and then 1% formaldehyde for 15 min at room temperature. Following cell lysis, chromatin was sheared using a Misonix 3000 probe sonicator (30 x 30 sec, 30 sec off). p65-bound chromatin was then immunoprecipitated using 8 micrograms anti-p65 (sc-372/C-20X) antibody. Following washing and reverse crosslinking, chromatin was purified using phenol-chloroform extraction. For RNA-seq: total mRNA was isolated using RNeasy Kit (Qiagen). DNA and mRNA libraries were created following standard Illumina protocols with PolyA capture for mRNA. ChIP-seq and RNA-seq; 2-lane flow cell (single-end 50 bp sequencing)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
26374339
Reads aligned (%)
91.1
Duplicates removed (%)
5.3
Number of peaks
1216 (qval < 1E-05)

hg38

Number of total reads
26374339
Reads aligned (%)
93.4
Duplicates removed (%)
4.0
Number of peaks
1223 (qval < 1E-05)

Base call quality data from DBCLS SRA