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| Status |
Public on Sep 29, 2011 |
| Title |
HudsonAlpha_ChipSeq_GM12878_Egr-1_v041610.1 |
| Sample type |
SRA |
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| Source name |
GM12878
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| 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
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| Biomaterial provider |
Coriell; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878
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| Treatment protocol |
None
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| Growth protocol |
GM12878_protocol.pdf
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| 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
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Data processing |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibTfbs
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| Submission date |
Sep 28, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
ENCODE DCC |
| E-mail(s) |
[email protected]
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| Organization name |
ENCODE DCC
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| Street address |
300 Pasteur Dr
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5120 |
| Country |
USA |
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| 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 |
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| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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