|
| Status |
Public on Feb 25, 2019 |
| Title |
chrRNA-seq_siPCF11_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: HeLa cells
molecule subtype: chromatin-bound RNA
genotype/treatment: PCF11 knock-down (50 nM)
|
| Treatment protocol |
siRNAs from Dharmacon were transfected for 48 hrs according to RNAiMAX reagent protocol at the concentrations indicated.
|
| Growth protocol |
HeLa cells were maintained in DMEM with 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Chromatin-bound semi-nascent RNAs were purified as described (Nojima et al., Cell, 2015, PMID: 25910207).
Chromatin RNA-Seq libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, NEB) according to manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were mapped with STAR 2.5b aligner with index generated from hg19 genome.
For visualisation genome-wide coverage were calculated and normalised for sequencing depth (rpm). BigWig files were generated to visualize the data in the UCSC browser.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files: genome-coverage files for all samples
|
| |
|
| Submission date |
Nov 19, 2018 |
| Last update date |
Feb 25, 2019 |
| Contact name |
Kinga Kamieniarz-Gdula |
| Organization name |
University of Oxford
|
| Department |
Sir William Dunn School of Pathology
|
| Street address |
South Parks Road
|
| City |
Oxford |
| ZIP/Postal code |
OX1 3RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE122708 |
Selective roles of vertebrate PCF11 in premature and full-length transcript termination (chromatin-bound RNA-seq) |
| GSE123105 |
Selective roles of vertebrate PCF11 in premature and full-length transcript termination |
|
| Relations |
| BioSample |
SAMN10441706 |
| SRA |
SRX5027104 |
