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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 29, 2011 |
| Title |
HudsonAlpha_ChipSeq_K562_USF-1_v041610.1 |
| Sample type |
SRA |
| |
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| Source name |
K562
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| Organism |
Homo sapiens |
| Characteristics |
datatype: ChipSeq
datatype description: Chromatin IP Sequencing
antibody antibodydescription: Rabbit polyclonal, USF-1 (C-20). Antibody Target: USF1
antibody targetdescription: The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types.
antibody vendorname: Santa Cruz Biotechnology
antibody vendorid: sc-229
controlid: SL2455
labexpid: SL3166,SL3163
replicate: 1,2
softwareversion: MACS
antibody: USF-1
antibody antibodydescription: Rabbit polyclonal, USF-1 (C-20).
antibody targetdescription: The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types.
antibody vendorname: Santa Cruz Biotech
antibody vendorid: sc-229
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: SL2455
labexpid: SL3163
replicate: 1
replicate description: tier 1
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| Biomaterial provider |
ATCC
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| Treatment protocol |
None
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| Growth protocol |
K562_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) |
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 |
| |
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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 |
SRX100486 |
| BioSample |
SAMN00738403 |
| Named Annotation |
GSM803441_hg19_wgEncodeHaibTfbsK562Usf1V0416101RawRep1.bigWig |
| Named Annotation |
GSM803441_hg19_wgEncodeHaibTfbsK562Usf1V0416101RawRep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM803441_hg19_wgEncodeHaibTfbsK562Usf1V0416101PkRep1.broadPeak.gz |
376.1 Kb |
(ftp)(http) |
BROADPEAK |
| GSM803441_hg19_wgEncodeHaibTfbsK562Usf1V0416101PkRep2.broadPeak.gz |
177.7 Kb |
(ftp)(http) |
BROADPEAK |
| GSM803441_hg19_wgEncodeHaibTfbsK562Usf1V0416101RawRep1.bigWig |
23.3 Mb |
(ftp)(http) |
BIGWIG |
| GSM803441_hg19_wgEncodeHaibTfbsK562Usf1V0416101RawRep2.bigWig |
11.7 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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