|
| Status |
Public on May 09, 2014 |
| Title |
NT-2 |
| Sample type |
SRA |
| |
|
| Source name |
Human cervical cancer
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
time: control
treatment: untreated
|
| Treatment protocol |
Cells were treated with DRB for 3hr and harvested after DRB removal. Cells were also labeld with 4sU for 8 min beofre harvested.
|
| Growth protocol |
HeLa cells were grown in DMEM supplemented with 10% heat-inactivated fetal bovine serum and penicillin-streptomycin antibiotics solution
|
| 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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Nascent RNA labled with 4sU
|
| 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)
For each experiment we constructed a genome-wide profile of the signal per disjoint 100 bp adjacent bins. The sum of each experiment was normalized to be 106
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file describe the transcription elongation velocity measured for all DRB-dependent genes.
|
| |
|
| Submission date |
Apr 26, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Gilad Fuchs |
| E-mail(s) |
gilad.fuchs@weizmann.ac.il
|
| Organization name |
Weizmann Institute of Science
|
| Street address |
Rehovot
|
| City |
Rehovot |
| ZIP/Postal code |
71600 |
| Country |
Israel |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE57116 |
4sUDRB-seq: measuring transcription elongation and initiation genomewide |
|
| Relations |
| BioSample |
SAMN02737861 |
| SRA |
SRX528190 |
