|
| Status |
Public on Jun 10, 2018 |
| Title |
siRNF20-384-mRNA |
| Sample type |
SRA |
| |
|
| Source name |
Human cervical carcinoma, HeLa cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
condition: siRNF20
replicate: 384
|
| Treatment protocol |
Cells were treated with DRB for 3hr and harvested after DRB removal. Cells were also labeld with 4sU for 12 min before harvested.
|
| Growth protocol |
HeLa cells were grown in DMEM supplemented with 10% bovine serum supplemented with antibiotics
|
| Extracted molecule |
total RNA |
| Extraction protocol |
4sU labled RNA was tagged with Biotion, and enriched with Streptavidin magnetic beads. cDNA libraries were prepared with Illumina TruSeq RNA sample preparation v2 kit according to the manufacturer's instructions but without the polyA isolation stage
4sUDRBseq: cDNA libraries were prepared with Illumina TruSeq RNA sample preparation v2 kit according to the manufacturer’s instructions but without the polyA isolation stage
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
mRNA for replicate 384, experiment siRNF20
|
| Data processing |
All reads were aligned to the human reference genome (hg19, GRCh37) using the bowtie 2 aligner with default parameters (only setting –N 1)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig (bw) files contains aligned read for 4sUDRBseq with masked exons
|
| |
|
| Submission date |
Jun 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Eran Rosenthal |
| E-mail(s) |
eran.rosenthal@mail.huji.ac.il
|
| Organization name |
Hebrew University
|
| Department |
Computer Science
|
| Lab |
Tommy Kaplan
|
| Street address |
Givat Ram
|
| City |
Jerusalem |
| ZIP/Postal code |
91904 |
| Country |
Israel |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE69738 |
Gene body H2B1ub regulates RNA Polymerase II pause release and is not needed for transcription elongation |
|
| Relations |
| BioSample |
SAMN03768422 |
| SRA |
SRX1055089 |
