|
| Status |
Public on Feb 01, 2011 |
| Title |
H3K4me3_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: E14 ES cells
chip antibody: anti-H3K4me3
antibody vender: Millipore
antibody catalog number: 07-473
antibody lot number: DAM1623866
|
| 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 II |
| |
|
| Description |
Chromatin IP against H3K4me3
|
| Data processing |
For H3K4me3 ChIP-seq, Sequence reads (36 bases) from the ChIP experiment were compiled, post-processed and aligned to UCSC MM8 using NOVOALIGN. Aligned reads were used to estimate the number of end-sequenced ChIP fragments that overlap any given genomic position (at 25 bp resolution). For each position, we counted the number of reads that were oriented towards it and closer than the average length of a library fragment (∼300 bp). The result is a high-resolution density map that can be viewed through the UCSC Genome Browser and is used for downstream analyses. Conversion of TSS between mm9 (Dpy-30) and mm8 (H3K4me3) genome built was performed using the UCSC liftover tool.
|
| |
|
| 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 |
GPL9250 |
| Series (1) |
| GSE26136 |
Mammalian Dpy-30 regulates genomic H3K4 methylation and is essential for ES cell fate specification |
|
| Relations |
| SRA |
SRX054581 |
| BioSample |
SAMN00254165 |
| Named Annotation |
GSM651193_ESC-H3K4me3-to_mm9.wig.gz |
| Named Annotation |
GSM651193_ESC-H3K4me3.track_def.wig.gz |
