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| Status |
Public on Sep 29, 2011 |
| Title |
HudsonAlpha_ChipSeq_SK-N-SH_RA_CTCF_v041610.2 |
| Sample type |
SRA |
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| Source name |
SK-N-SH_RA
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| Organism |
Homo sapiens |
| Characteristics |
datatype: ChipSeq
datatype description: Chromatin IP Sequencing
cell description: neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)
antibody antibodydescription: Rabbit polyclonal. Antibody Target: CTCF
antibody targetdescription: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
antibody vendorname: Millipore
antibody vendorid: 07-729
controlid: SL2905
labexpid: SL2914,SL2906
replicate: 1,2
softwareversion: MACS
antibody antibodydescription: rabbit polyclonal
antibody targetdescription: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
antibody vendorname: Millipore
antibody vendorid: 07-729
treatment: None
treatment description: No special treatment or protocol applies
protocol: v041610.2
protocol description: 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)
controlid: SL2905
labexpid: SL2906
replicate: 1
replicate description: tier 1
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| Biomaterial provider |
ATCC
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| Treatment protocol |
None
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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
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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 (1) |
| GSE32465 |
Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB |
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| Relations |
| SRA |
SRX100378 |
| BioSample |
SAMN00738295 |
| Named Annotation |
GSM803333_hg19_wgEncodeHaibTfbsSknshraCtcfV0416102RawRep1.bigWig |
| Named Annotation |
GSM803333_hg19_wgEncodeHaibTfbsSknshraCtcfV0416102RawRep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM803333_hg19_wgEncodeHaibTfbsSknshraCtcfV0416102PkRep1.broadPeak.gz |
580.2 Kb |
(ftp)(http) |
BROADPEAK |
| GSM803333_hg19_wgEncodeHaibTfbsSknshraCtcfV0416102PkRep2.broadPeak.gz |
639.4 Kb |
(ftp)(http) |
BROADPEAK |
| GSM803333_hg19_wgEncodeHaibTfbsSknshraCtcfV0416102RawRep1.bigWig |
20.3 Mb |
(ftp)(http) |
BIGWIG |
| GSM803333_hg19_wgEncodeHaibTfbsSknshraCtcfV0416102RawRep2.bigWig |
29.9 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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