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| Status |
Public on Oct 21, 2013 |
| Title |
S. cerevisiae rep6 |
| Sample type |
SRA |
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| Source name |
S. cerevisiae _yeast cells
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YHL068
genotype/variation: wild type
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| Growth protocol |
Cultures were grown at 25°C in YPD medium to log phase (between 0.65-0.75 OD at 600 nm).
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
Sample 10
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| 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.
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| Submission date |
Jun 22, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Yulia Mostovoy |
| Organization name |
University of California, San Francisco
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| Lab |
Kwok lab
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| Street address |
555 Mission Bay Blvd South
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL13272 |
| Series (1) |
| GSE38875 |
Expression evolution in gene groups: Inferring non-neutral regulatory change in pathways from transcriptional profiling data |
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| Relations |
| SRA |
SRX155605 |
| BioSample |
SAMN01057198 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM951301_cer_for_bay_2.counts.txt.gz |
20.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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