|
| Status |
Public on Apr 03, 2009 |
| Title |
DPY-27 emb replicate 1 GFP |
| Sample type |
SRA |
| |
|
| Source name |
dpy-27 transgenic worm OP32
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: OP32
growth stage: embryo
antibody: anti-GFP
|
| Treatment protocol |
Resuspend embryo or Lava stage samples in 2% formaldehyde solution. Place on a shaker (50-100 rpm) and incubate for 30 minutes at room temperature. Wash samples once with 100 mM Tris pH 7.5 (to quench excess formaldehyde), 2 times with M9 Buffer, and once with FA buffer supplemented with protease inhibitors.
|
| Growth protocol |
Transgenic worms were routinelly grow on plates to obtain as many adults with embryos. Bleach to obtain embryos. Hatch overnight in M9 Buffer to obtain L1s. Wash L1s and put into 500 ml liquid media (S medium+1X PSN antibiotics and nystatin) and grow at 20 oC in an incubator shaking at 230 rpm. Add concentrated E Coli for food as necessary during growth. It takes around 2.5-3 days to obtain adults with embryos. Collect adults and bleach to obtain embryos. Spin down embryos at 3000 g for 3 minutes. Resuspend pellet (embryos) and wash 2 more times with M9 Buffer. Continue with the same wash and cross-linking steps.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was sheared to 200-800 bp using a Branson sonifier microtip, immunoprecipitated using anti-GFP antibody, purified for the DNA fragments bound by transcription factor, and sequenced it using Illumina Genome Analyzers.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against anti-GFP
|
| Data processing |
Sequence reads were aligned to the reference genome, and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200 bp.
|
| |
|
| Submission date |
Apr 01, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Flora Vaccarino |
| Organization name |
Yale University
|
| Department |
Child Study Center
|
| Lab |
Vaccarino
|
| Street address |
230 South Frontage Road
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06520 |
| Country |
USA |
| |
|
| Platform ID |
GPL9309 |
| Series (1) |
| GSE15501 |
Identification of transcription factor DPY-27 binding sites |
|
| Relations |
| SRA |
SRX003830 |
| BioSample |
SAMN02197808 |
