|
| Status |
Public on May 03, 2018 |
| Title |
siPNPase_INPUT |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells, siPNPase, input
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
treatment: siPNPase
antibody: none
|
| Treatment protocol |
HeLa cells treated with siLuc (control), siSUV3 or siPNPase.
|
| Growth protocol |
HeLa cells were grown as a monolayer at 37ºC, under 5% CO2 in high glucose DMEM medium supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
HeLa cell lysate was prepared with NP-40 lysis buffer and cellular dsRNA were pulled down with J2 antibody (anti-dsRNA mAb J2, Prod. Nr. 10010500 from Scicons). RNA was extracted using Trizol reagent for library preparation.
Libraries were prepared with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina, v1.0 (cat. no. E7420) according to the manufacturer's guidelines.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-sequencing reads were trimmed using Cutadapt and then mapped to the human reference genome with Bowtie2.
Aligned reads were processed to only include properly paired, uniquely mapped reads with no more than 2 mismatches using SAMtools.
Data were scaled to library size (genomeCoverageBed) using Bedtools.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: BigWig files containing read densities from RNA-seq experiments.
|
| |
|
| Submission date |
Feb 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicholas Proudfoot |
| E-mail(s) |
nicholas.proudfoot@path.ox.ac.uk
|
| Organization name |
Sir William Dunn School of Pathology, University of Oxford
|
| Street address |
South Parks Road
|
| City |
Oxford |
| ZIP/Postal code |
OX1 3RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE94957 |
Mitochondrial dsRNA triggers antiviral signalling in humans |
|
| Relations |
| BioSample |
SAMN06339648 |
| SRA |
SRX2565087 |
