Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRCA1

Cell type

Cell type Class
Neural
Cell type
SH-EP
NA
NA

Attributes by original data submitter

Sample

source_name
SH-EP-NMYCER
cell line
SH-EP-NMYCER
treatment
EtOH
treatment2
flavopiridol
shRNA
none
antibody
BRCA1 (Bethyl, A300-000A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were treated with 1% formaldehyde for 10 min at 37 °C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <500 bp using a Branson sonifier. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and purified with Qiagen gel extraction kit. DNA fragments were amplified by 18 cycles of PCR and library size was tested with the Biorad Experion system. The amount of library DNA was quantified using a picogreen assay

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
13988876
Reads aligned (%)
68.6
Duplicates removed (%)
31.1
Number of peaks
736 (qval < 1E-05)

hg38

Number of total reads
13988876
Reads aligned (%)
69.7
Duplicates removed (%)
30.1
Number of peaks
748 (qval < 1E-05)

Base call quality data from DBCLS SRA