|
| Status |
Public on Jan 01, 2017 |
| Title |
ubc9-1, untreated, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Cell
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: ubc9-1
treatment: No treatment
|
| Treatment protocol |
100 nM rapamycin for 30 min
|
| Growth protocol |
YPD medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy kit (Qiagen) and RNAs between 50 and 100 nt were selected.
Library construction and sequencing were performed by BGI
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads were filtered and trimmed using a custom script (BGI)
Reads were mapped against the R64-1-1 genome assembly using Tophat2 (v. 2.0.13) with default settings.
The number of reads per gene in the Ensemble 75 gene build were counted using featureCounts (v. 1.4.6-p3) in paired-end mode and with -t gene and -M options.
Only features <200 nt were used for further analysis
Genome_build: R64-1-1.75
Supplementary_files_format_and_content: Tab-delimited text files include raw counts and the normalized CPM values for each Sample
|
| |
|
| Submission date |
Aug 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Håvard Aanes |
| E-mail(s) |
Havard.Aanes@rr-research.no
|
| Organization name |
Oslo University Hospital
|
| Department |
Dept of microbiology
|
| Lab |
Klungland Lab
|
| Street address |
Sognsvannsveien 20
|
| City |
Oslo |
| ZIP/Postal code |
0372 |
| Country |
Norway |
| |
|
| Platform ID |
GPL21656 |
| Series (1) |
| GSE85622 |
TORC1 shapes the SUMO proteome to control RNA polymerase III activity |
|
| Relations |
| BioSample |
SAMN05578060 |
| SRA |
SRX2023637 |
