|
| Status |
Public on May 19, 2020 |
| Title |
Sample 2_Wild-type;MMS treated;Biorep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Wild-type_MMS treated_whole cell
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain background: BY4741
genotype/variation: wild type
treatment: methyl methanesulfonate (MMS) for 90min
|
| Treatment protocol |
Cells were treated with MMS for 90 min at 30 degrees C.
|
| Growth protocol |
Cells were grown in YPD to OD~0.5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using hot phenol followed by chloroform extraction and ethanol precipitation.
polyA enriched libraries were prepared from total RNA using Oligo-dT beads. Samples were prepared according to library kit manufacturer’s protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
sample.2_wt_90_a
|
| Data processing |
RNA-seq reads were then aligned to the Ensembl release 76 (GCA_000146045.2) with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.23.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
Genome_build: Ensembl release 76 (GCA_000146045.2)
Supplementary_files_format_and_content: gene counts
|
| |
|
| Submission date |
May 18, 2020 |
| Last update date |
May 19, 2020 |
| Contact name |
Liewei Leo Yan |
| Organization name |
Washington University in St Louis
|
| Department |
Biology
|
| Lab |
Zaher Lab
|
| Street address |
1 brookings dr.
|
| City |
st louis |
| State/province |
MO |
| ZIP/Postal code |
63139 |
| Country |
USA |
| |
|
| Platform ID |
GPL27812 |
| Series (1) |
| GSE150790 |
Ribosome-quality control antagonizes the activation of integrated-stress response on colliding ribosomes |
|
| Relations |
| BioSample |
SAMN14967007 |
| SRA |
SRX8360028 |
