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Sample GSM803434 Query DataSets for GSM803434
Status Public on Sep 29, 2011
Title HudsonAlpha_ChipSeq_GM12878_Egr-1_v041610.1
Sample type SRA
 
Source name GM12878
Organism Homo sapiens
Characteristics datatype: ChipSeq
datatype description: Chromatin IP Sequencing
cell description: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus
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 vendorname: Santa Cruz Biotechnology
antibody vendorid: sc-110
controlid: SL1613
labexpid: SL3579,SL3828
replicate: 1,2
softwareversion: MACS
antibody antibodydescription: Rabbit polyclonal, EGR-1 (588).
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 vendorname: Santa Cruz Biotech
antibody vendorid: sc-110
treatment: None
treatment description: No special treatment or protocol applies
protocol: v041610.1
protocol description: 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)
controlid: SL1613
labexpid: SL3579
replicate: 1
replicate description: tier 1
Biomaterial provider Coriell; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878
Treatment protocol None
Growth protocol GM12878_protocol.pdf
Extracted molecule genomic DNA
Extraction 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
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Data processing http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibTfbs
 
Submission date Sep 28, 2011
Last update date May 15, 2019
Contact name ENCODE DCC
E-mail(s) encode-help@lists.stanford.edu
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
 
Platform ID GPL9052
Series (2)
GSE32465 Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB
GSE51334 DNA replication-timing boundaries separate stable chromosome domains with cell-type-specific functions
Relations
SRA SRX100479
BioSample SAMN00738396
Named Annotation GSM803434_hg19_wgEncodeHaibTfbsGm12878Egr1V0416101RawRep1.bigWig
Named Annotation GSM803434_hg19_wgEncodeHaibTfbsGm12878Egr1V0416101RawRep2.bigWig

Supplementary file Size Download File type/resource
GSM803434_hg19_wgEncodeHaibTfbsGm12878Egr1V0416101PkRep1.broadPeak.gz 161.1 Kb (ftp)(http) BROADPEAK
GSM803434_hg19_wgEncodeHaibTfbsGm12878Egr1V0416101PkRep2.broadPeak.gz 261.5 Kb (ftp)(http) BROADPEAK
GSM803434_hg19_wgEncodeHaibTfbsGm12878Egr1V0416101RawRep1.bigWig 17.2 Mb (ftp)(http) BIGWIG
GSM803434_hg19_wgEncodeHaibTfbsGm12878Egr1V0416101RawRep2.bigWig 20.0 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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