|
| Status |
Public on Jul 03, 2013 |
| Title |
CAGE egfp |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
barcode: ATGCAGCAG
cell line: HeLa
cell type: egfp control
|
| Treatment protocol |
22nM siRNA transfection (doule hit)
|
| Growth protocol |
HeLa cells grown in DMEM medium supplemented with 10% fetal bovine serum at 37°C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Purelink (Ambion)
CAGE (PMID: 21938627)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
For the 5' end, an extra G in position 10 of the reads, right after the barcode, needs to be trimmed. This is due to an artifact in the reverse transcription of the capped G. For the 3'end, the last 8 nt also needs to be trimmed due to 3' end adaptors.
|
| Data processing |
CAGE: basecalling by CASAVA version 1.8.2. The first 10 nt from 5'end and the last 8nt from 3'end are trimmed off (check sample description). All the reads are then filtered by fastq_quality_filter (fastx_toolkit) using -q 30 -p 50 and mapped to hg19 by bowtie version 0.12.7 using --strata --best -k 10. Only 5'end of single mapped reads are used in the analysis.
|
| |
|
| Submission date |
Jun 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Aino Inkeri Järvelin |
| Organization name |
University of Oxford
|
| Department |
Department of Biochemistry
|
| Street address |
South Parks Road
|
| City |
Oxford |
| ZIP/Postal code |
OX1 3QU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE48286 |
High-throughput sequencing of PROMPT-enriched samples. |
|
| Relations |
| BioSample |
SAMN02213670 |
| SRA |
SRX315103 |
