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Sample GSM951294 Query DataSets for GSM951294
Status Public on Oct 21, 2013
Title S. paradoxus rep1
Sample type SRA
 
Source name S. paradoxus_yeast cells
Organism Saccharomyces paradoxus
Characteristics strain: CBS 432
genotype/variation: wild type
Growth protocol Cultures were grown at 25°C in YPD medium to log phase (between 0.65-0.75 OD at 600 nm).
Extracted molecule polyA RNA
Extraction protocol Total RNA was isolated by the hot acid phenol method' and treated with Turbo DNA-free (Ambion) according to the manufacturer's instructions. Libraries for 3’end RNA-seq were generated according to the published protocol (Yoon and Brem, RNA 2010) with the following modifications: 1) AmpureXP beads (Beckman) were used to clean up enzymatic reactions; 2) the gel purification and size-selection step was removed; 3) the oligo-dT primer used for cDNA synthesis was phosphorothioated at position ten (TTTTTTTTTT*TTTTTTTTTTVN, V=A,C,G, N=A,C,G,T, *=phosphorothioate linkage, Integrated DNA Technologies); and 4) 12 PCR cycles were performed.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description Sample 3
Data processing Basecalling with Illumina CASAVA version 1.7
Reads were mapped to the corresponding species’ genome from http://www.saccharomycessensustricto.org/ using Bowtie version 0.12.7 with default settings and flags -m1 -X1000.
Filtering: To ensure that poly-A tails did not originate from stretches of As or Ts encoded endogenously in the genome, we discarded reads whose stretch of As or Ts contained more than 50% matches to the reference genome. In order to filter for potential oligo-dT mispriming during cDNA synthesis, we also discarded reads that contained 10 or more As in the 20 nucleotides upstream of their transcription termination site.
GC correction: For each lane of sequencing, we grouped sets of overlapping reads and normalized abundance according to GC content of the overlapping region using full-quantile normalization as implemented in the package EDASeq. Normalized abundance was divided by raw abundance to generate a weight that was assigned to every read in the group. These weights were used in place of raw read counts in all downstream analyses.
Genome_build: Assemblies from http://www.saccharomycessensustricto.org
Supplementary_files_format_and_content: Abundance measurements were calculated as follows: for each gene, we searched for reads that had mapped to either its sense or antisense region, and obtained GC-normalized read counts for each such feature by summing the weighted abundance of the reads.
 
Submission date Jun 22, 2012
Last update date May 15, 2019
Contact name Yulia Mostovoy
Organization name University of California, San Francisco
Lab Kwok lab
Street address 555 Mission Bay Blvd South
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
 
Platform ID GPL15725
Series (1)
GSE38875 Expression evolution in gene groups: Inferring non-neutral regulatory change in pathways from transcriptional profiling data
Relations
SRA SRX155598
BioSample SAMN01057191

Supplementary file Size Download File type/resource
GSM951294_par_1.counts.txt.gz 20.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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