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| Status |
Public on May 22, 2012 |
| Title |
USC_ChipSeq_GM12878_TR4_std |
| Sample type |
SRA |
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| Source name |
GM12878
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| Organism |
Homo sapiens |
| Characteristics |
lab: USC
lab description: Farnham - University of Southern California
datatype: ChipSeq
datatype description: Chromatin IP Sequencing
cell: GM12878
cell organism: human
cell description: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus
cell karyotype: normal
cell lineage: mesoderm
cell sex: F
treatment: None
treatment description: No special treatment or protocol applies
antibody: TR4
antibody antibodydescription: Rabbit polyclonal. Antibody Target: TR4
antibody targetdescription: (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus.
antibody vendorname: Donated by Dr. J.D.Engel, University of Michigan
antibody vendorid: TR4
control: std
control description: Standard input signal for most experiments.
control: std
control description: Standard input signal for most experiments.
controlid: wgEncodeEH000625
labversion: Fragmented using Bioruptor, precipitated with StaphA PeakSeq 1.0 (fdr 0.001), samples were 71% and 72% matching in the top 40% overlap analysis.
replicate: 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=wgEncodeSydhTfbs
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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=wgEncodeSydhTfbs
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| Submission date |
May 22, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
ENCODE DCC |
| E-mail(s) |
[email protected]
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| Organization name |
ENCODE DCC
|
| Street address |
300 Pasteur Dr
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5120 |
| Country |
USA |
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| Platform ID |
GPL9052 |
| Series (2) |
| GSE31477 |
ENCODE Transcription Factor Binding Sites by ChIP-seq from Stanford/Yale/USC/Harvard |
| GSE51334 |
DNA replication-timing boundaries separate stable chromosome domains with cell-type-specific functions |
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| Relations |
| SRA |
SRX150559 |
| BioSample |
SAMN01001019 |
| Named Annotation |
GSM935480_hg19_wgEncodeSydhTfbsGm12878Tr4StdSig.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM935480_hg19_wgEncodeSydhTfbsGm12878Tr4StdPk.narrowPeak.gz |
36.7 Kb |
(ftp)(http) |
NARROWPEAK |
| GSM935480_hg19_wgEncodeSydhTfbsGm12878Tr4StdSig.bigWig |
427.2 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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