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Sample GSM651192 Query DataSets for GSM651192
Status Public on Feb 01, 2011
Title Dpy-30_ChIP-seq
Sample type SRA
Source name Embryonic stem cells
Organism Mus musculus
Characteristics cell type: E14 ES cells
chip antibody: anti-Dpy-30
antibody provider: unreleased product from Bethyl Laboratories, developed by Christina Hughes (David Allis lab, Rockefeller University) through Bethyl
Treatment protocol For Dpy-30 ChIP-seq, cells in monolayer culture were washed twice with 1 x PBS and fixed with 2 mM Disuccinimidyl glutarate (DSG) for 1 hour at room temperature. After removal of DSG and washing with PBS, cells were further fixed with 1.2% Formaldehyde in PBS/1 mM MgCl2 for 15 min at room temperature. For H3K4me3 ChIP-seq, cells were fixed with 1% Formaldehyde for 10 min at room temperature.
Growth protocol E14 cells were cultured on 0.1% gelatinized tissue-culture plates in complete ESC growth medium supplemented with LIF
Extracted molecule genomic DNA
Extraction protocol Chromatin was sonicated nuclei and immunoprecipitated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description Chromatin IP against Dpy-30
Data processing For Dpy-30 ChIP-seq, the sequencing was performed on an Illumina Genome Analyzer IIx for 36 cycles. Image analysis and base calling were performed using Solexa pipeline V1.6 and short reads (pass quality filter) were aligned to mouse NCBI build 37 (UCSC MM9) using NOVOALIGN. Unique alignments were used for peak calling of the ChIP regions using MACS v1.3.7.1. Sequences were extended 296 bp, and then the whole genome was scanned by 300 bp windows. Statistically significant ChIP-seq enrichment regions (peaks) were identified by comparison to a Poissonian background model, using a p-value threshold of 10-5. Nearest TSSs (600 kb window) around calling peaks were then searched using the newest ENSEMBL database.
Submission date Jan 06, 2011
Last update date May 15, 2019
Contact name Hao Jiang
Organization name Rockefeller University
Lab Roeder Lab
Street address 1230 York Ave
City New York
State/province NY
ZIP/Postal code 10065
Country USA
Platform ID GPL11002
Series (1)
GSE26136 Mammalian Dpy-30 regulates genomic H3K4 methylation and is essential for ES cell fate specification
SRA SRX054580
BioSample SAMN00254164

Supplementary file Size Download File type/resource
GSM651192_ChIPSeq_Dpy-30_Mus_musculus_MM9_novoalign_genome_alignment.txt.gz 922.9 Mb (ftp)(http) TXT
GSM651192_ChIPSeq_Dpy-30_Mus_musculus_MM9_peaks.bed.gz 251.4 Kb (ftp)(http) BED
GSM651192_treat_afterfiting_chr1.wig.gz 19.6 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chr10.wig.gz 13.6 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chr11.wig.gz 15.5 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chr12.wig.gz 11.8 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chr13.wig.gz 12.4 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chr14.wig.gz 11.5 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chr15.wig.gz 10.9 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chr16.wig.gz 9.6 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chr17.wig.gz 10.3 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chr18.wig.gz 9.2 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chr19.wig.gz 7.0 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chr2.wig.gz 20.2 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chr3.wig.gz 15.1 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chr4.wig.gz 16.6 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chr5.wig.gz 16.8 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chr6.wig.gz 18.3 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chr7.wig.gz 15.4 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chr8.wig.gz 17.3 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chr9.wig.gz 14.3 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chrM.wig.gz 4.1 Kb (ftp)(http) WIG
GSM651192_treat_afterfiting_chrX.wig.gz 6.9 Mb (ftp)(http) WIG
GSM651192_treat_afterfiting_chrY.wig.gz 106.2 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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