Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRCA1

Cell type

Cell type Class
Uterus
Cell type
HeLa
Primary Tissue
Cervix
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
HeLa-S3
biomaterial_provider
ATCC
lab
Stanford
lab description
Snyder - Stanford University
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell
HeLa-S3
cell organism
human
cell description
cervical carcinoma
cell karyotype
cancer
cell lineage
ectoderm
cell sex
F
treatment
None
treatment description
No special treatment or protocol applies
antibody
BRCA1_(A300-000A)
antibody antibodydescription
Rabbit polyclonal recognizing a region between residue 1800 and the C-terminus (residue 1863) of human Breast Cancer Gene 1. Antibody Target: BRCA1
antibody targetdescription
Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers.
antibody vendorname
Bethyl Labratories
antibody vendorid
A300-000A
control
IgG-rab
control description
Input signal from Normal Rabbit IgG ChIP-seq.
control
IgG-rab
control description
Input signal from Normal Rabbit IgG ChIP-seq.
controlid
wgEncodeEH000744
replicate
1

Sequenced DNA Library

library_name
GSM935552: Stanford_ChipSeq_HeLa-S3_BRCA1_(A300-000A)_IgG-rab
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
57882602
Reads aligned (%)
71.6
Duplicates removed (%)
14.5
Number of peaks
16129 (qval < 1E-05)

hg38

Number of total reads
57882602
Reads aligned (%)
73.1
Duplicates removed (%)
13.3
Number of peaks
16300 (qval < 1E-05)

Base call quality data from DBCLS SRA