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Sample GSM2863256 Query DataSets for GSM2863256
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

Supplementary file Size Download File type/resource
GSM2863256_pat1-0-R3_neg.BedGraph.gz 3.8 Mb (ftp)(http) BEDGRAPH
GSM2863256_pat1-0-R3_pos.BedGraph.gz 4.0 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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