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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 22, 2011 |
| Title |
RasV12_H3K27me3 |
| Sample type |
SRA |
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| Source name |
Mouse embryonic fibroblast
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| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse embryonic fibroblast
treatment: infected with activated RasV12-expressing retrovirus
antibody: H3K27me3
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells on a plate were cross-linked with 1% formaldehyde for 10 min at room temperature and were prepared for ChIP. ChIP using anti-Ezh2 antibody (#39103, Active Motif, rabbit polyclonal) was performed. Briefly, crosslinked cell lysates underwent fragmentation by sonication and incubated with antibodies bound to protein A-sepharose bease (50% slurry) overnight at 4 ºC. The beads were washed several times and eluted with elution buffer (1%SDS, 0.1 M NaHCO3). The eluates were treated with 1.5 μg of pronase 2 hr at 42 ºC then incubated at 65 ºC over night to reverse the crosslinks. The ChIP’ed DNA was purified by phenol/chroloform treatment and precipitated with LiCl and 70% ethanol. Sample preparation for ChIP-sequencing was performed according to the manufacturer's instructions (Ilumina), and sequencing was performed using Solexa Giga sequencer. Briefly, size fractionated DNA was extracted and a single adenosine was added using Klenow exo– (3' and 5' exo minus; Illumina). Illumina adaptors were then added and DNA was subjected to 20 cycles of PCR according to manufacturer's instructions. We then purified DNA and performed cluster generation and 36 cycles of sequencing on the Illumina cluster station and 1G Analyzer following the manufacturer's instructions. Sequences were mapped to the Build #36 (mm8) reference mouse genome.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Chromatin immunoprecipitation (ChIP)-Solexa analysis of H3K27me3 for oncogenic Ras-induced senescent MEF cells
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| Data processing |
Bed files
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| Submission date |
Sep 18, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Atsushi Kaneda |
| E-mail(s) |
kaneda@genome.rcast.u-tokyo.ac.jp
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| Organization name |
The University of Tokyo
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| Department |
RCAST
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| Lab |
Genome Science Division
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| Street address |
4-6-1 Komaba
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| City |
Meguro-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
153-8904 |
| Country |
Japan |
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| Platform ID |
GPL9185 |
| Series (1) |
| GSE18125 |
Epigenetic regulation of Bmp2 and Smad6 in Ras-induced senescence |
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| Relations |
| SRA |
SRX019220 |
| BioSample |
SAMN00011316 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM454433_RasV12_K27_sort.bed.gz |
59.8 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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