|
| Status |
Public on Feb 28, 2014 |
| Title |
Wild Type |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
cell type: human embryonic kidney cells
exposed to: None
exposure length: 0hr
|
| Treatment protocol |
When the cells were about 80% confluent, the medium in one well was replaced and 100 μg/ml ethyl methanesulfonate (EMS; Sigma) was added. Cells were grown in the presence of EMS for 24 hours followed by a 24 hour recovery period in fresh medium.
|
| Growth protocol |
The human embryonic kidney cell line HEK293 was maintained and passaged according to established cell culture conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA and DNA were isolated using Trizol according to standard methodology. The RNA was quality tested and size selected on a denaturing polyacrylamide gel (19-29 bases).
Tagged 3’ adaptors and 5’ adaptors were ligated to the recovered RNA to ensure strand specificity. The material was used for cDNA synthesis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
NG-5562_1
|
| Data processing |
Read Alignment: Bowtie v 1.0.0, default parameters
Unaligned reads filtered: Samtools v0.1.18, options: view -F 0x04
Mapped reads intersecting with exons & miRNAs found: BEDTools (intersectBed) v2.12.0 - target BED files from UCSC genome browser
Count reads intersecting with features (standard Linux tools - awk, sort, uniq)
Genome_build: hg18
Supplementary_files_format_and_content: BED, reads intersecting with exons and miRNAs, Excel file (read counts)
|
| |
|
| Submission date |
Dec 04, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Simon Cockell |
| E-mail(s) |
[email protected]
|
| Organization name |
Newcastle University
|
| Street address |
Framlington Place
|
| City |
Newcastle |
| ZIP/Postal code |
NE2 4HH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE52996 |
Contribution of natural antisense transcription to an endogenous siRNA signature in human cells |
|
| Relations |
| BioSample |
SAMN02436935 |
| SRA |
SRX387227 |
