|
| Status |
Public on Nov 26, 2013 |
| Title |
FAIRE_DL23_nt |
| 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
|
| 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 |
library strategy: FAIRE-seq
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.
FAIRE sample was generated from 10x106 DLD1-F3 cells as described in detail (Simon et al., 2012). Briefly, cells were crosslinked in 1% formaldehyde (for 5 minutes at room temperature), lysed, collected in buffer with protease inhibitors (Roche) and dounced with a tight pestle. Nuclei were collected through centrifugation, lysed and DNA was sheared using Biorupter Sonicator. FAIRE DNA was obtained through phenol/chloroform/isoamyl alcohol and chloroform/isoamyl (SIGMA) extraction. DNA was treated with DNase-free RNase and proteinase K (Ambion), decrosslinked overnight at 65C and purified with Qiaquick PCR purification kit (Qiagen).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| 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 |
SAMN02335196 |
| SRA |
SRX340065 |
