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| Status |
Public on Sep 12, 2012 |
| Title |
DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom(Duke/UNC/UTA) |
| Project |
ENCODE
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| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
These tracks display a synthesis of evidence from different assays as part of the four Open Chromatin track sets. This track displays open chromatin regions and/or transcription factor binding sites identified in multiple cell types by one or more complementary methodologies, DNaseI hypersensitivity (HS) (Duke DNaseI HS), Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (UNC FAIRE), and chromatin immunoprecipitation (ChIP) for select regulatory factors (UTA TFBS). Each methodology was performed on the same cell type using identical growth conditions. (Note: Data for some or all ChIP experiments may not be available for all cell types). Regions that overlap between methodologies identify regulatory elements that are cross-validated indicating high confidence regions. In addition, multiple lines of evidence suggest that regions detected by a single assay (e.g., DNase-only or FAIRE-only) are also biologically relevant (Song et al., submitted).
DNaseI HS data: DNaseI is an enzyme that has long been used to map general chromatin accessibility, and DNaseI "hypersensitivity" is a feature of active cis-regulatory sequences.The use of this method has led to the discovery of functional regulatory elements that include promoters, enhancers, silencers, insulators, locus control regions, and novel elements. DNaseI hypersensitivity signifies chromatin accessibility following binding of trans-acting factors in place of a canonical nucleosome.
FAIRE data: FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements) is a method to isolate and identify nucleosome-depleted regions of the genome. FAIRE was initially discovered in yeast and subsequently shown to identify active regulatory elements in human cells (Giresi et al., 2007). Similar to DNaseI HS, FAIRE appears to identify functional regulatory elements that include promoters, enhancers, silencers, insulators, locus control regions and novel elements.
ChIP data: ChIP (Chromatin Immunoprecipitation) is a method to identify the specific location of proteins that are directly or indirectly bound to genomic DNA. By identifying the binding location of sequence-specific transcription factors, general transcription machinery components, and chromatin factors, ChIP can help in the functional annotation of the open chromatin regions identified by DNaseI HS mapping and FAIRE.
Input data: As a background control experiment, we sequenced the input genomic DNA sample that was used for ChIP. Crosslinked chromatin is sheared and the crosslinks are reversed without carrying out the immunoprecipitation step. This sample is otherwise processed in a manner identical to the ChIP sample as described below. The input track is useful in revealing potential artifacts arising from the sequence alignment process such as copy number differences between the reference genome and the sequenced samples, as well as regions of poor sequence alignability.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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| Overall design |
For each site, the maximum F-Seq Density Signal value has been calculated for each assay that was performed in that cell type. F-Seq employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Significant regions, or peaks, were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05 (DNaseI HS, ChIP) or 0.1 (FAIRE) threshold were considered significant. See assay specific description pages ( Duke DNaseI HS, UNC FAIRE and UTA TFBS) for more details.
A Fisher's Combined P-value for DNaseI HS and FAIRE was calculated using Fisher's combined probability test. First, a test statistic is calculated using the formula x^2 = -2*sum(ln(pi)) where pi are the p-values calculated for DNaseI HS and FAIRE. X2 follows a chi-squared distribution, thus a combined p-value can be assigned to this test statistic.
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| Web link |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromSynth
http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
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| Contributor(s) |
Furey T, Zhang Z, Song L, Crawford G, Giresi P, Lieb J, Liu Z, McDaniell R, Lee B, Iyer V, Flicek P, Keefe D, Birney E, Graf S |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA63443 |
| Submission date |
Sep 12, 2012 |
| 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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| Platforms (1) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
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| Samples (17)
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| GSM1002651 |
Duke_Combined_GM12878_wgEncodeOpenChromSynth |
| GSM1002652 |
Duke_Combined_PanIslets_wgEncodeOpenChromSynth |
| GSM1002653 |
Duke_Combined_HeLa-S3_wgEncodeOpenChromSynth |
| GSM1002654 |
Duke_Combined_HepG2_wgEncodeOpenChromSynth |
| GSM1002655 |
Duke_Combined_H1-hESC_wgEncodeOpenChromSynth |
| GSM1002656 |
Duke_Combined_HUVEC_wgEncodeOpenChromSynth |
| GSM1002657 |
Duke_Combined_K562_wgEncodeOpenChromSynth |
| GSM1002658 |
Duke_Combined_NHEK_wgEncodeOpenChromSynth |
| GSM1002659 |
Duke_Combined_Urothelia_UT189_wgEncodeOpenChromSynth |
| GSM1002660 |
Duke_Combined_HeLa-S3_IFNa4h_wgEncodeOpenChromSynth |
| GSM1002661 |
Duke_Combined_HTR8svn_wgEncodeOpenChromSynth |
| GSM1002662 |
Duke_Combined_Gliobla_wgEncodeOpenChromSynth |
| GSM1002663 |
Duke_Combined_GM19239_wgEncodeOpenChromSynth |
| GSM1002664 |
Duke_Combined_GM18507_wgEncodeOpenChromSynth |
| GSM1002665 |
Duke_Combined_GM12892_wgEncodeOpenChromSynth |
| GSM1002666 |
Duke_Combined_GM12891_wgEncodeOpenChromSynth |
| GSM1002667 |
Duke_Combined_Medullo_wgEncodeOpenChromSynth |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE40833_RAW.tar |
128.2 Mb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Raw data provided as supplementary file |
| Processed data provided as supplementary file |
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