|
| Status |
Public on Jul 02, 2014 |
| Title |
CAGE Egfp rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
barcode: ATGCAGCAG
treatment: Egfp knock down (control)
cell line: HeLa
|
| Treatment protocol |
22nM siRNA transfection (double 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 Genome Analyzer IIx |
| |
|
| 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 11 nt from 5'end and the last 6 nt from 3'end are trimmed off. 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 uniquely mapped reads are used in the analysis.
Genome_build: hg19
Supplementary_files_format_and_content: CAGE bed files contain positions of 5' ends of unique locations of CAGE tags and the number of CAGE tags at that position (score column).
|
| |
|
| Submission date |
Jul 01, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Robin Andersson |
| E-mail(s) |
robin@binf.ku.dk
|
| Organization name |
University of Copenhagen
|
| Street address |
Ole Maaloes Vej 5
|
| City |
Copenhagen N |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE58991 |
Nuclear stability and transcriptional directionality separate functionally distinct RNA species |
| GSE62047 |
Nuclear stability and transcriptional directionality separate functionally distinct RNA species. |
|
| Relations |
| BioSample |
SAMN02899070 |
| SRA |
SRX643186 |
