|
| Status |
Public on Nov 26, 2013 |
| Title |
RNA_DL23_4OHT_8h_Rep2 |
| 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 |
polyA RNA |
| Extraction protocol |
Sequencing libraries were constructed using SOLiD® Total RNA-Seq Kit (Life technologies) according to the standard protocol recommendations for low input and sequenced on SOLiD sequencer in a multiplexed way to produce 50-bp long reads.
To isolate polyadenylated and capped RNA, total RNA was purified using Poly(A)Purist MAG Kit (Life Technologies) according to manufacturer's instructions. Isolated RNA was subsequently re-purified using mRNA-ONLY Eukaryotic mRNA Isolation Kit (Epicentre).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| 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 |
SAMN02335199 |
| SRA |
SRX340067 |
