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Sample GSM991016 Query DataSets for GSM991016
Status Public on Nov 21, 2012
Title mRNA enriched, WT -DTT Rep 2 (rRNA depleted)
Sample type SRA
 
Source name WT -DTT
Organism Schizosaccharomyces pombe
Characteristics genotype/variation: WT
stress: control (-DTT)
Treatment protocol Samples were taken after treatment with 2mM DTT for 1 hour.
Growth protocol Cells were cultured in YE5S media (rich media). Samples were taken from mid-log growing cells.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cells using hot phenol method. PolyA+ mRNA were enriched by two sequential rounds of oligo-dT (Invitrogen) selection. rRNA depletion was performed by depletion of ll RNA smaller than 200nt (mirVana miRNA Purification Kit (Ambion) followed by two rounds of subtractive hybridization using Ribominus EukaryoteKit for RNA-seq (Invitrogen). To sequence 2',3'-cyclic phosphate cleavage products tRNA ligase was used to selectively ligate an RNA linker to all 2',3'-cyclic phosphates in total RNA. Deep-sequencing libraries were constructed as described in Ingolia et al, 2011. To capture 2',3'cyclic-phosphate 3' ends the libraries were constructed according to Schutz et al., 2010.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description total RNA (rRNA depleted)
mRNA enriched from total RNA by removing ribosomal RNA
Data processing Basecalls performed using CASAVA version 1.4
The resulting sequences were aligned using the following method: the linker sequences at the 3’ends were removed prior to alignment.
The SOAP2.20 was used to align the sequence reads (allowing no more than 2 total mismatches)
Reads after linker removal were aligned against a library of S. pombe rRNA and tRNA sequences. Reads with any alignment against rRNA and tRNA were eliminated from further analysis.
the none-rRNA and none-tRNA reads were aligned against the S. pombe genomic sequences.
reads with no alignment against S. pombe genomics sequences were re-aligned against the library of pombe processed protein-coding transcripts.
Genome_build: Recent genome build (09/05/2011) from the PomBase
Supplementary_files_format_and_content: wig
 
Submission date Aug 22, 2012
Last update date May 15, 2019
Contact name Philipp Kimmig
Organization name University of California, San Francisco
Department Biochemistry and Biophysics
Lab Peter Walter lab
Street address Genentech Hall N316, 600 16th Street
City San Francisco
State/province CA
ZIP/Postal code 94158-2517
Country USA
 
Platform ID GPL13988
Series (1)
GSE40298 The unfolded protein response in fission yeast modulates stability of select mRNAs to maintain protein homeostasis
Relations
SRA SRX180547
BioSample SAMN01121953

Supplementary file Size Download File type/resource
GSM991016_WT_-rRNA_+strand_repl2.wig.gz 2.0 Mb (ftp)(http) WIG
GSM991016_WT_-rRNA_-strand_repl2.wig.gz 2.0 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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