Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
EGR1

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
GSM1010730
antibody antibodydescription
Rabbit polyclonal, EGR-1 (588). Antibody Target: EGR1
antibody targetdescription
Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner.
antibody vendorid
sc-110
antibody vendorname
Santa Cruz Biotechnology
antibody
Egr-1
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
SL218
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL482
protocol description
a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers)
protocol
PCR2x
replicate
3
softwareversion
MACS
treatment description
No special treatment or protocol applies
treatment
None

Sequenced DNA Library

library_name
GSM1010730: HudsonAlpha_ChipSeq_GM12878_Egr-1_PCR2x
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
43030947
Reads aligned (%)
44.7
Duplicates removed (%)
7.7
Number of peaks
4012 (qval < 1E-05)

hg38

Number of total reads
43030947
Reads aligned (%)
45.6
Duplicates removed (%)
7.3
Number of peaks
3798 (qval < 1E-05)

Base call quality data from DBCLS SRA