Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRCA1

Cell type

Cell type Class
Blood
Cell type
GM12878
Tissue
blood
Lineage
mesoderm
Description
B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

Attributes by original data submitter

Sample

source_name
GM12878
biomaterial_provider
GM12878
lab
Stanford
lab description
Snyder - Stanford University
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell
GM12878
cell organism
human
cell description
B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus
cell karyotype
normal
cell lineage
mesoderm
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-mus
control description
Input signal from Normal Mouse IgG ChIP-seq.
control
IgG-mus
control description
Input signal from Normal Mouse IgG ChIP-seq.
controlid
wgEncodeEH000706
replicate
1

Sequenced DNA Library

library_name
GSM935377: Stanford_ChipSeq_GM12878_BRCA1_(A300-000A)_IgG-mus
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
52825334
Reads aligned (%)
87.4
Duplicates removed (%)
4.8
Number of peaks
2171 (qval < 1E-05)

hg38

Number of total reads
52825334
Reads aligned (%)
89.5
Duplicates removed (%)
3.5
Number of peaks
1809 (qval < 1E-05)

Base call quality data from DBCLS SRA