Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RUNX3

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

GEO Accession
GSM1010893
antibody antibodydescription
Mouse monoclonal IgG, raised against amino acids 191-300 of recombinant RUNX3 of human origin. Antibody Target: RUNX3
antibody targetdescription
This gene encodes a member of the runt domain-containing family of transcription factors. A heterodimer of this protein and a beta subunit forms a complex that binds to the core DNA sequence 5'-PYGPYGGT-3' found in a number of enhancers and promoters, and can either activate or suppress transcription. It also interacts with other transcription factors. It functions as a tumor suppressor, and the gene is frequently deleted or transcriptionally silenced in cancer. Multiple transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq)
antibody vendorid
sc-101553
antibody vendorname
Santa Cruz Biotechnology
antibody
RUNX3_(SC-101553)
cell description
B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus
cell karyotype
normal
cell lineage
mesoderm
cell organism
human
cell sex
F
cell
GM12878
controlid
SL6022
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL8128,SL7898
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
GSM1010893: HudsonAlpha_ChipSeq_GM12878_RUNX3_(SC-101553)_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
97406780
Reads aligned (%)
74.7
Duplicates removed (%)
12.6
Number of peaks
101395 (qval < 1E-05)

hg38

Number of total reads
97406780
Reads aligned (%)
75.5
Duplicates removed (%)
13.2
Number of peaks
98402 (qval < 1E-05)

Base call quality data from DBCLS SRA