Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GABPA

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

GEO Accession
GSM1010864
antibody antibodydescription
Mouse monoclonal, GABPa(G-1), IgG1. Antibody Target: GABP
antibody targetdescription
The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence.
antibody vendorid
sc-28312
antibody vendorname
Santa Cruz Biotechnology
antibody
GABP
cell description
mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis
cell karyotype
cancer
cell lineage
ectoderm
cell organism
human
cell sex
F
cell
MCF-7
controlid
SL16758,SL13504
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL14683,SL13459
protocol description
Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)
protocol
v042211.1
replicate
1,2
softwareversion
MACS
treatment description
No special treatment or protocol applies
treatment
None

Sequenced DNA Library

library_name
GSM1010864: HudsonAlpha_ChipSeq_MCF-7_GABP_v042211.1
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibTfbs

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
65149875
Reads aligned (%)
62.5
Duplicates removed (%)
19.5
Number of peaks
16578 (qval < 1E-05)

hg38

Number of total reads
65149875
Reads aligned (%)
63.5
Duplicates removed (%)
18.5
Number of peaks
16614 (qval < 1E-05)

Base call quality data from DBCLS SRA