|
| Status |
Public on Nov 26, 2013 |
| Title |
CHIP_DL23_4OHT_4h_H3K4me1 |
| Sample type |
SRA |
| |
|
| Source name |
DL23 cell line with pcDNA3-HA-FOXO33-ER
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DL23 cell line with pcDNA3-HA-FOXO33-ER
chip antibody: H3K4me1
chip antibody vendor: Abcam
chip antibody cat. #: ab8895
|
| Growth protocol |
DLD1 and DLD1-F3 cells 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 sequencer to produce 50-bp long reads.
4-hydroxy-tamoxifen (4OHT) from Sigma, was dissolved in ethanol and added to cells at a final concentration of 1uM. Cells were treated with PKB inhibitor VIII (Santa Cruz) at a concentration of 10uM. Cells were grown in the absence or 4 hour presence of 4OHT or PKB inhibitor. Three independent batches of chromatin were obtained for all three conditions and mixed, with a total of 80x106 cells per IP. IPs were performed for 16h with the following antibodies: 2.5 ug of H3K4me1, H3K4me3 and H3K27ac and total H3 from Abcam (ab8895, ab8580 and ab4729, ab1791) and 16ug of αFOXO3 (Santa Cruz, H144) for the FOXO3-ER (2) ChIP-seq. The second H3K27ac(2) ChIP-seq was performed on an independent fourth batch of chromatin.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Data processing |
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin, 2009). Non-uniquely placed reads were discarded.
Cisgenome v2.0 software package was used to calculate reads per 1000 base pairs of transcript per million reads sequenced (RPKM) values for all RefSeq annotated genes.
Genome_build: hg19
Supplementary_files_format_and_content: alignment file (chr;start;end;strand)
|
| |
|
| Submission date |
Aug 27, 2013 |
| 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) |
| GSE50243 |
FOXO3 selectively amplifies enhancer activity to establish target gene regulation. |
|
| Relations |
| BioSample |
SAMN02335201 |
| SRA |
SRX340058 |
