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| Status |
Public on May 22, 2012 |
| Title |
USC_ChipSeq_MCF-7_HA-E2F1_UCDavis |
| Sample type |
SRA |
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| Source name |
MCF-7
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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: MCF-7
cell organism: human
cell description: mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis
cell karyotype: cancer
cell lineage: ectoderm
cell sex: F
treatment: None
treatment description: No special treatment or protocol applies
antibody: HA-E2F1
antibody antibodydescription: Mouse Monoclonal antibody HA.11 clone 16B12 was raised against the twelve amino acid peptide CYPYDVPDYASL. This second-generation HA antibody is an excellent substitute for the 12CA5 monoclonal antibody. The HA.11 antibody recognizes the influenza hemagglutinin epitope (YPYDVPDYA) which has been used extensively as a general epitope tag in expression vectors. The extreme specificity of the antibody allows unambiguous identification and quantitative analysis of the tagged protein. The HA.11 antibody recognizes HA epitopes located in the middle of protein sequences as well as at the N- or C-terminus. Antibody Target: HA-E2F1
antibody targetdescription: The HA-E2F1 protein is a derivative of E2F1, a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionary conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. This version of E2F1 includes an N terminal HA tag and a modified ER ligand binding domain to allow regulated translocation to the nucleus.
antibody vendorname: Covance
antibody vendorid: MMS-101P
control: UCDavis
control description: Input library was prepared at UC Davis.
control: UCDavis
control description: Input library was prepared at UC Davis.
controlid: wgEncodeEH000762
labversion: MCF-7 cells stably expressed a tagged HA-E2F1 were fragmented using Bioruptor, precipitated with StaphA and an antibody to the HA tag,
replicate: 1
softwareversion: PeakSeq1.0 (fdr 0.001)
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| Biomaterial provider |
ATCC
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| Treatment protocol |
None
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| Growth protocol |
MCF-7_Farnham_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
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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) |
| 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 |
SRX150556 |
| BioSample |
SAMN01001016 |
| Named Annotation |
GSM935477_hg19_wgEncodeSydhTfbsMcf7Hae2f1UcdSig.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM935477_hg19_wgEncodeSydhTfbsMcf7Hae2f1UcdPk.narrowPeak.gz |
310.9 Kb |
(ftp)(http) |
NARROWPEAK |
| GSM935477_hg19_wgEncodeSydhTfbsMcf7Hae2f1UcdSig.bigWig |
371.1 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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