|
| Status |
Public on Sep 29, 2015 |
| Title |
HEK293 nuclear RNA seq |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 nuclear RNA seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell line/type: HEK293 cells
subcellular fraction: nuclear
dicer knockdown: No
|
| Treatment protocol |
Dicer depleted over 5 days when stated
|
| Growth protocol |
10% FCS in DMEM
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
PolyA+ RNA and prepared with Ion Proton whole transcriptome v2 kit
Trizol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
293_nucleus_RNAseq
|
| Data processing |
Alignment with bowtie2
Selection for poly(A) supporting reads containing 2 or more non-genomically encoded A's
Conversion to bigwig file
Normalisation of bigwig files to reads per million
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files containing the normalised (RPM) data
|
| |
|
| Submission date |
May 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jonathan Neve |
| Organization name |
Oxford University
|
| Department |
Biochemistry
|
| Lab |
Furger
|
| Street address |
South Parks Road
|
| City |
Oxford |
| ZIP/Postal code |
OX1 3QU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE68671 |
Differential regulation of alternatively polyadenylated isoforms |
|
| Relations |
| BioSample |
SAMN03646996 |
| SRA |
SRX1021914 |
