|
| Status |
Public on Jul 31, 2009 |
| Title |
CEH-14 L2 replicate 2 GFP |
| Sample type |
SRA |
| |
|
| Source name |
OP73, CEH-14:GFP:3xFLAG animals
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: OP73
growth stage: L2
antibody: anti-GFP
|
| Treatment protocol |
L2 animals were crossedliked in 2% formaldehyde solution for 30 minutes at room temperature, washed one time 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 and then stored at -80 oC.
|
| Growth protocol |
CEH-14:GFP:3xFLAG animals were grown on NGM plates to obtain gravity adults with embryos and then bleached to obtain embryos. Embryos were hatched overnight in M9 Buffer to obtain snychronized L1animals. L1 animals were then transfered into 500 ml liquid media (S medium+1X PSN antibiotics and nystatin) and grew at 20 oC in an incubator shaking at 230 rpm. Concentrated E. Coli were added as necessary during growth. When reached at L2 stage, animals were collected, washed, and cross-linked.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was sheared to 200-800 bp using a Branson sonifier microtip, immunoprecipitated using anti-GFP antibody and purified using Qiangen PCR purification kit. The protocol for library preparation was adapted from the protocol "Preparing Samples for sequencing genomic DNA" by Illumina.
|
| |
|
| 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 |
Jul 31, 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) |
| GSE17454 |
Identification of transcription factor CEH-14 binding sites in C.elegans |
|
| Relations |
| SRA |
SRX015094 |
| BioSample |
SAMN00007178 |
