|
| Status |
Public on Oct 25, 2011 |
| Title |
UT-A_ChipSeq_GM12878_CTCF |
| Sample type |
SRA |
| |
|
| Source name |
GM12878
|
| 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
treatment: None
treatment description: No special treatment or protocol applies
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: wgEncodeEH000528
labversion: baseAlignCounts.pl v 1,fseq v 1.84, iff_GM12878,p-value cutoff: 0.05,1% ENCODE array platform validation tests
replicate: 1,3,2
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: GM12878/Input
labversion: align_on_cluster_bwa.pl v 1
replicate: 1
replicate description: tier 1
|
| Biomaterial provider |
Coriell; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878
|
| Growth protocol |
GM12878_protocol.pdf
|
| 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=wgEncodeOpenChromChip
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromChip
|
| |
|
| Submission date |
Oct 25, 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 |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE33213 |
Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin) |
| GSE51334 |
DNA replication-timing boundaries separate stable chromosome domains with cell-type-specific functions |
|
| Relations |
| Reanalyzed by |
GSM1002651 |
| SRA |
SRX103011 |
| BioSample |
SAMN00744181 |
| Named Annotation |
GSM822312_hg19_wgEncodeOpenChromChipGm12878CtcfBaseOverlapSignal.bigWig |
| Named Annotation |
GSM822312_hg19_wgEncodeOpenChromChipGm12878CtcfSig.bigWig |
