|
| Status |
Public on Nov 15, 2012 |
| Title |
endogenous_FOXO3_ChIP_seq |
| Sample type |
SRA |
| |
|
| Source name |
endogenous_FOXO3_ChIP_seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DLD1 cell line
chip antibody: aFOXO3 (H144)
chip antibody vendor: Santa Cruz
|
| Treatment protocol |
4-hydroxy-tamoxifen (4OHT) was Sigma, was dissolved in ethanol and added to cells at a final concentration of 1uM. Cells were treated with LY 294002 at a concentration of 10 µM.
|
| Growth protocol |
DLD1 colon carcinoma cell line and DL23 clone containing pcDNA3-HA-FOXO33-ER or pcDNA3-ER-DBD-NLS were grown on RPMI-1640 medium with 10% FCS and standard supplements.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was additionally sheared, end-repaired, sequencing adaptors were ligated and the library was amplified by LMPCR. After LMPCR, the library was purified and checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel and sequenced on SOLiD/AB sequencer to produce 50-bp long reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Description |
DLD1_enER
|
| Data processing |
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin 2009).
Genome Build:
DLD1VIII1haFOXO3n29.txt: hg19
|
| |
|
| Submission date |
Nov 15, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Michal Mokry |
| E-mail(s) |
m.mokry@umcutrecht.nl
|
| Organization name |
Wilhelmina Children's Hospital, University Medical Center Utrecht
|
| Street address |
Lundlaan 6
|
| City |
Utrecht |
| ZIP/Postal code |
3584 EA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16288 |
| Series (1) |
| GSE35486 |
Genome wide analysis of FOXO3 transcription regulation through RNA pol II profiling |
|
| Relations |
| SRA |
SRX204674 |
| BioSample |
SAMN01814535 |
