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Sample GSM2304419 Query DataSets for GSM2304419
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) stefan.bresson@gmail.com
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

Supplementary file Size Download File type/resource
GSM2304419_total_RNA_8.bw 35.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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