|
| Status |
Public on Jul 18, 2018 |
| Title |
pat1_t0_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
pat1
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: pat1 (BY4741; MATa; ura3delta_0; leu2delta_0; his3delta_1; met15delta_0; YCR077c::kanMX4)
time: 0
|
| Treatment protocol |
To induce osmotic stress, KCl was added to the culture at 0.6M final concentration for 30 minutes.
|
| Growth protocol |
Saccharomyces cerevisiae cells were grown at 30°C till mid-log phase (OD600 0.4-0.5) in synthetic medium supplemented with appropriate amino acids and 2% glucose as the carbon source.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested and pellets were frozen in liquid nitrogen and kept at -80°C until further processing. Total RNA was extracted from yeast cells using phenol:chloroform extraction.
5PSeq methods was performed as previously described (PMID: 26820793) with minor modifications. 6µg of total RNA was used as input. After single-stranded RNA ligation, partial rRNA depletion was performed using Ribo-Zero Magnetic Gold Kit (Epicentre). 5PSeq libraries were PRC amplified (19 cycles), pooled and size selected (300-500nt). Samples were sequenced using a NextSeq500 producing single-end 75 reads.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Library strategy: 5P-Seq
Read demultiplexed using Illumina BaseSpace servers. Illumina BaseSpace FASTQ Generation. Version: 1.0.0
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 Hisat2 with default parameters (except limiting the maximum intron size to 2kb). 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 por positive and negative strand
|
| |
|
| Submission date |
Nov 21, 2017 |
| Last update date |
May 15, 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) |
| GSE107250 |
Study of ribosome dynamics after osmotic stress in Lsm1 and Pat1 deletions |
|
| Relations |
| BioSample |
SAMN08052641 |
| SRA |
SRX3414689 |
