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Series GSE32218 Query DataSets for GSE32218
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 and
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.
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Contributor(s) Snyder M, Weissman S, Cayting P
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BioProject PRJNA63471
Submission date Sep 19, 2011
Last update date Nov 20, 2019
Contact name ENCODE DCC
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)
SRA SRP008276

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Supplementary file Size Download File type/resource
GSE32218_RAW.tar 4.5 Gb (http)(custom) TAR (of BIGWIG, NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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