|
| Status |
Public on Jan 05, 2011 |
| Title |
Drosophila_larvae_wt_H3K9me2_ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
3rd instart Drosophila larvae
|
| Organism |
Drosophila melanogaster |
| Characteristics |
h3k9me2 antibody: 07-441 Upstate antibody
genotype: wild type
|
| Treatment protocol |
In vivo experiment of wildtype vs mutant (fly EHMT)
|
| Growth protocol |
Larvae were cultured on standard medium (cornmeal/sugar/agar) at 25 degrees, 45-60% humidity and 12 hour light/dark cycle
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Third instar larvae were homogenized in PBS followed by crosslinking with 1% formaldehyde. Crosslinked chromatin was fragmented by sonicating four times for eight minutes (high power, 30 seconds on/off) with a Bioruptor (Diagenode). Chromatin immunoprecipitation was performed with anti-H3K9me2 antibodies and Prot A/G beads (Santa Cruz) were used to capture antibody bound chromatin.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Chromatin IP against H3K9me2
|
| Data processing |
Reads (36 bp) were aligned to the fly (Drosophila Melanogaster) reference genome. Sequences were aligned to the human BDGP R5/dm3 reference genome using the Illumina Analysis Pipeline allowing one mismatch. Unless specified otherwise, only the tags uniquely aligning to the genome were considered for further analysis. The 36 bp sequence reads were directionally extended to 300 bp, corresponding to the length of the original fragments used for sequencing. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing the data in the UCSC Genome Browser. All ChIP-Seq sequence analyses were conducted based on the Apr. 2006 Drosophila melanogaster draft assembly (BDGP Release 5) with Release 5.12 annotations (Oct. 2008) accessed from the UCSC (assembly April 2006) Genome Browser.
|
| |
|
| Submission date |
Jun 18, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Hendrik Marks |
| E-mail(s) |
h.marks@ncmls.ru.nl
|
| Organization name |
Radboud University Nijmegen, RIMLS
|
| Department |
Molecular Biology
|
| Street address |
Geert Grooteplein 26/28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525GA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL9061 |
| Series (1) |
| GSE22447 |
ChIP-Seq sequencing of H3K9me2 in third instar Drosophila larvae |
|
| Relations |
| SRA |
SRX022334 |
| BioSample |
SAMN00015358 |
