|
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 |
E-mail(s) |
hjiang@rockefeller.edu
|
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 |
|
Relations |
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 Selector |
Processed data provided as supplementary file |
Raw data are available in SRA |