|
| Status |
Public on Sep 20, 2011 |
| Title |
Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale |
| Project |
Mouse ENCODE
|
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
This track shows probable locations of the specified histone modifications in the given cell types as determined by chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq). Each experiment is associated with an input signal, which represents the control condition where immunoprecipitation with non-specific immunoglobulin was performed in the same cell type. For each experiment (cell type vs. antibody) this track shows a graph of enrichment for histone modification (Signal), along with sites that have the greatest evidence of histone modification, as identified by the PeakSeq algorithm (Peaks).
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 |
Cells were grown according to the approved ENCODE cell culture protocols. For details on the chromatin immunoprecipitation protocol used, see Euskirchen et. al., (2007), Rozowsky et. al. (2009) and Auerbach et. al. (2009).
DNA recovered from the precipitated chromatin was sequenced on the Illumina (Solexa) sequencing platform and mapped to the genome using the Eland alignment program. ChIP-seq data was scored based on sequence reads (length ~30 bps) that align uniquely to the human genome. From the mapped tags a signal map of ChIP DNA fragments (average fragment length ~ 200 bp) was constructed where the signal height is the number of overlapping fragments at each nucleotide position in the genome.
For each 1 Mb segment of each chromosome, a peak height threshold was determined by requiring a false discovery rate <= 0.01 when comparing the number of peaks above said threshold to the number of peaks obtained from multiple simulations of a random null background with the same number of mapped reads (also accounting for the fraction of mapable bases for sequence tags in that 1 Mb segment). The number of mapped tags in a putative binding region is compared to the normalized (normalized by correlating tag counts in genomic 10 kb windows) number of mapped tags in the same region from an input DNA control. Using a binomial test, only regions that have a p-value <= 0.01 are considered to be significantly enriched compared to the input DNA control.
|
| Web link |
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeSydhHist
http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
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| |
|
| Contributor(s) |
Snyder M, Weissman S, Cayting P |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA63471 |
| |
| Submission date |
Sep 19, 2011 |
| Last update date |
Nov 20, 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 |
| |
|
| Platforms (2) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
|
| Samples (22)
|
| GSM798323 |
Yale_ChipSeq_MEL_Input_DMSO_2.0pct_IgG-Yale |
| GSM798324 |
Yale_ChipSeq_MEL_H3K4me3_IgG-Yale (superseded by GSM1003753) |
| GSM798325 |
Yale_ChipSeq_MEL_Input_IgG-Yale (superseded by GSM1003747) |
| GSM798326 |
Yale_ChipSeq_CH12_Input_IgG-Yale |
| GSM798327 |
Yale_ChipSeq_CH12_H3K4me3_IgG-Yale |
| GSM798328 |
Yale_ChipSeq_MEL_H3K4me3_DMSO_2.0pct_IgG-Yale (superseded by GSM1003754) |
| GSM1003744 |
Stanford_ChipSeq_MEL_H3K4me1_IgG-rab |
| GSM1003745 |
Stanford_ChipSeq_MEL_H3K27me3B_DMSO_2.0pct_std |
| GSM1003746 |
Stanford_ChipSeq_ES-E14_Input_std (superseded by GSE136425) |
| GSM1003747 |
Stanford_ChipSeq_MEL_Input_IgG-rab (superseded by GSE94229) |
| GSM1003748 |
Stanford_ChipSeq_MEL_H3K9me3_DMSO_2.0pct_std |
| GSM1003749 |
Stanford_ChipSeq_MEL_H3K36me3B_DMSO_2.0pct_std |
| GSM1003750 |
Stanford_ChipSeq_ES-E14_H3K4me1_std |
| GSM1003751 |
Stanford_ChipSeq_ES-E14_H3K9me3_std |
| GSM1003752 |
Stanford_ChipSeq_MEL H3K27me3 IgG-rab (was Stanford_ChipSeq_MEL_H3K27ac_IgG-rab) (superseded by GSE94230) |
| GSM1003753 |
Stanford_ChipSeq_MEL_H3K4me3_IgG-rab (superseded by GSE94231) |
| GSM1003754 |
Stanford_ChipSeq_MEL_H3K4me3_DMSO_2.0pct_std (superseded by GSE94233) |
| GSM1003755 |
Stanford_ChipSeq_MEL_H3K9me3_IgG-rab |
| GSM1003756 |
Stanford_ChipSeq_ES-E14_H3K4me3_std |
| GSM1003757 |
Stanford_ChipSeq_MEL_H3K4me1_DMSO_2.0pct_std |
| GSM1003758 |
Stanford_ChipSeq_MEL_Input_DMSO_2.0pct_std (superseded by GSE94232) |
| GSM1201760 |
Stanford_ChipSeq_MEL_H3K27me3_IgG-rab |
|
| Relations |
| SRA |
SRP008276 |
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