|
| Status |
Public on Oct 01, 2019 |
| Title |
CHX_rrp6∆_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
yeast cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: rrp6[delta]::KanMX
parental strain: BY4741(MATa his3[delta]1 leu2[delta]0 met15[delta]0 ura3[delta]0)
treatment: Cycloheximide treatment
|
| Treatment protocol |
Cells were incubated with 0.1 mg/ml final cycloheximide for 10 minutes prior to harvesting.
|
| Growth protocol |
Saccharomyces cerevisiae grown in YPD at 30°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from yeast cells using the hot phenol procedure. The amount of RNA was quantified in a Nanodrop 2000 Spectrophotometer (Thermo Scientific) and RNA integrity was checked by agarose gel electrophoresis.
5PSeq methods was performed as previously described (PMID: 26820793). 6µg of total RNA was used as input. In brief a RNA oligo (rP5_RND) containing an Illumina adaptor and unique molecular identifiers (UMI) was ligated to the intermediates of mRNA co-translation degradation (5’P). Ribosomal RNA was depleted using Ribo-Zero Magnetic Gold Kit (Illumina).Libraries were PCR amplified (14 cycles). Ampure beads size selected libraries with a length of 300-500 nt were sent for sequencing (llumina NextSeq 500 instrument).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base-calling was done using bcl2fastq v2.20.0.422 with one mismatch
For each read we trimmed the first 8 nt (UMI, unique molecular identifier) and align the rest to S. cerevisiae genome (version R64-1-1) using STAR 2.5.3a default settings except AlignIntronMax(2500). Reads with the same 5’mapping site and UMI were considered PCR duplicates and omitted from the analysis.
Genome_build: S. cerevisiae R64-1-1
Supplementary_files_format_and_content: Bedgraph files for UMI collapsed reads for positive and negative strand
|
| |
|
| Submission date |
Mar 20, 2019 |
| Last update date |
Oct 03, 2019 |
| Contact name |
Vicent Pelechano |
| E-mail(s) |
vicente.pelechano.garcia@ki.se
|
| Organization name |
ScilifeLab - Karolinska Institutet
|
| Department |
MTC
|
| Street address |
Nobels väg 16
|
| City |
Solna |
| ZIP/Postal code |
SE-17177 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL19756 |
| Series (1) |
| GSE128599 |
Effect of cycloheximide in the co-translation mRNA degradation pattern in set2D and rrp6D strains |
|
| Relations |
| BioSample |
SAMN11178442 |
| SRA |
SRX5547703 |
