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| Status |
Public on Sep 20, 2010 |
| Title |
CY2706 (TRA1-wt) |
| Sample type |
SRA |
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| Source name |
whole cell lysate
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: CY2706
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| Growth protocol |
Yeast cells, CY2706 and CY3003, were grown at 30˚ in YP media containing 2% glucose to an A600 = 2.0.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified from 108 cells after glass bead disruption as described previously (MUTIU and BRANDL 2005; MUTIU et al. 2007b). RNA integrity numbers of greater than 8.9 were determined for each RNA sample using an Agilent 2100 Bioanalyzer at the The London Regional Genomics Centre Microarray Facility. mRNA-Seq libraries were constructed and sequencing were performed on the Illumina/Solexa Genome Analyzer II platform at the DNA Facility at Iowa State University. The CY2706 and CY3003 samples were each run on a single Illumina GAII lane, producing 13014880 reads for CY2706 and 11156078 reads for CY3003 that were 35 nucleotides long.
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| Library strategy |
FL-cDNA |
| Library source |
synthetic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Data processing |
Alignment: The sequencing reads were mapped onto the Saccharomyces cerevisiae genomic sequence (May, 1, 2009) using the novoindex and novoalign programs with the default parameters, except that reads mapping to two or more places in the genome were placed at one position at random. With this option novoalign marks a read as uniquely or repetitively mapping in the genome; only uniquely mapping reads were used for the subsequent analysis and 83% and 84% of the CY2706 and CY3003 reads were mapped uniquely. Uniquely mapped reads were placed into bins composed of protein-coding genes, tRNA and rRNA genes as defined by the gff file. Only reads that did not overlap the start or end position of the gene were counted and reads mapping to the top and bottom strands were tabulated separately.
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| Submission date |
Oct 15, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Brandl |
| Organization name |
University of Western Ontario
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| Department |
Biochemistry
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| Lab |
Brandl
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| Street address |
1151 Richmond St.
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| City |
London |
| State/province |
Ontario |
| ZIP/Postal code |
N6A 5C1 |
| Country |
Canada |
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| Platform ID |
GPL9377 |
| Series (1) |
| GSE18591 |
Gene profiling of TRA1 and tra1-L3733A |
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| Relations |
| SRA |
SRX018735 |
| BioSample |
SAMN00010880 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM462310_2706_gene_count.txt.gz |
158.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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