|
| Status |
Public on Jun 06, 2009 |
| Title |
H3K4me3_ChIP-Seq_XT67E1_undiff |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C3H/Pgk*129
cell type: ES-cells
antibody: H3K4me3 Diagenode
|
| Treatment protocol |
ES cells were either treated with atRA for 4 days or grown to EBs (removal of LIF) for 10 days
|
| Growth protocol |
ES cells were cultured in normal cell culture containing ES-grade serum supplemented with LIF. These cells were grown on gelatin-coated plates
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was fixed in 1% formaldehyde for 10 minutes, sheared to 200-700bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against H3K4me3
|
| Data processing |
Reads (32 bp) were aligned to the Mouse (Mus muscules) reference genome. Tracks for the different cell lines or antibodies were equalized for the total number of mapped tags by random removal of sequenced tags. Wiggle files were generated from these bed files.
All ChIP-Seq sequence analyses were conducted based on Mus musculus NCBI m37 genome assembly (MM9) accessed from the Ensembl (release 49) or the UCSC (assembly July 2007) genome browsers.
|
| |
|
| Submission date |
Apr 24, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
H.G. Stunnenberg |
| E-mail(s) |
h.stunnenberg@ncmls.ru.nl
|
| Phone |
+31-24-3610520
|
| Organization name |
Radboud University
|
| Department |
Department of Molecular Biology (274)
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
USA |
| |
|
| Platform ID |
GPL9185 |
| Series (2) |
| GSE15814 |
High resolution analysis of epigenetic changes associated with X inactivation, ChIP-Seq |
| GSE15884 |
High resolution analysis of epigenetic changes associated with X inactivation |
|
| Relations |
| SRA |
SRX006967 |
| BioSample |
SAMN02197783 |
| Named Annotation |
GSM397402_XT67E1_undiff_H3K4me3-ChIP-Seq.wig.gz |
