|
| Status |
Public on Jan 01, 2017 |
| Title |
total_RNA_8 |
| Sample type |
SRA |
| |
|
| Source name |
total RNA 8
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
sample type: poly(A) RNA
|
| Growth protocol |
Yeast cells were grown in SD -TRP media containing 2% glucose overnight and inoculated into fresh media at a starting OD600 of 0.05. Cells were grown for about 7 hours (until OD600=0.5) and either UV crosslinked (0 timepoint) or filtered and transferred to SD -TRP containing 2% glycerol and ethanol instead of glucose. Cells were UV crosslinked 4 or 8 minutes later.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot phenol RNA extraction followed by rRNA depletion using the RiboZero kit (Epicentre)
RNA libraries were prepared using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Data was preprocessed using the fastx package
Fastq files were split by barcode using pyBarcodeFilter.py in the pyCRAC package (Webb, et al, 2014). -m 0
Reads were aligned to the genome using Novoalign. -r Random
Reads were counted using pyReadCounter. --sense
Sequences were plotted along the genome using pyGTF2bedgraph
Genome_build: EF4.68
Supplementary_files_format_and_content: bedgraph or bigwig files showing the distribution of reads across the yeast genome
|
| |
|
| Submission date |
Sep 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Stefan Bresson |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Edinburgh
|
| Department |
Wellcome Trust Centre for Cell Biology
|
| Lab |
Tollervey Lab
|
| Street address |
Max Born Crescent, Swann 5.1
|
| City |
Edinburgh |
| State/province |
Scotland |
| ZIP/Postal code |
EH9 3BF |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE86483 |
Nuclear RNA decay pathways aid rapid remodeling of gene expression in yeast |
|
| Relations |
| BioSample |
SAMN05732400 |
| SRA |
SRX2141161 |
