Antigen

Antigen Class

TFs and others

Antigen

RELA

Cell type

Cell type Class

Breast

Cell type

HMEC

Primary Tissue

Breast

Tissue Diagnosis

Normal

Sample

source_name

Human mammary epithelial cells (HMEC)

treatment

untreated

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

23444285

Reads aligned (%)

96.8

Duplicates removed (%)

5.6

Number of peaks

1108 (qval < 1E-05)

hg38

Number of total reads

23444285

Reads aligned (%)

97.8

Duplicates removed (%)

4.2

Number of peaks

1098 (qval < 1E-05)