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| Status |
Public on Feb 22, 2010 |
| Title |
S. cerevisiae and S. bayanus L4 |
| Sample type |
SRA |
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| Source name |
biological replicate 2, run at UCB
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| Organism |
Saccharomyces bayanus x Saccharomyces cerevisiae |
| Characteristics |
strain: OZY27
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| Growth protocol |
Strain OZY27, a hybrid of S. cerevisiae (isogenic to W303; his3 leu2 lys2 trp1 ura3) and S. bayanus (derived from CBS 4001; ade2 his3 lys2), was kindly provided by O. Zill, UC Berkeley. For each of two biological replicates, an OZY27 culture was grown to log phase at 25°C in YPD media.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by the hot acid phenol method and treated with Turbo DNase (Ambion) according to the manufacturer’s instructions. A Solexa/Illumina 1G Genome Analyzer library was constructed for each biological replicate as described.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
process data counts are in L4 column of gene_level_statistics file
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| Data processing |
We downloaded 4,853 ortholog pairs (http://www.broad.mit.edu/regev/orthogroups/orthologs.html) and, in each, converted the S. cerevisiae reference sequence to that of the W303 strain using the sequence of the latter from Liti et al., Nature 2009. For each lane, 30-bp reads were mapped to either strand of the ortholog pair set using Bowtie, allowing no mismatches between the read and the reference sequence. As the S. bayanus and S. cerevisiae species are close in sequence, we ensured specificity of the expression measures by requiring that a read assigned to a certain location was likely to have originated from that location and not as a result of sequencing errors. Specifically, for each position in the combined orfeome, we determined whether the read starting at that location was uniquely-mappable (2), i.e., had an edit distance of 2 or greater to any other position in the combined (double-stranded) reference orfeome or genome. The combined orfeome consists of all 4,853 S. bayanus and S. cerevisiae ortholog pairs; the combined genome consists of the concatenation of the S. bayanus (http://downloads.yeastgenome.org/sequence/fungal_genomes/S_bayanus/WashU/contig/) and S. cerevisiae (ftp://ftp.yeastgenome.org/yeast/data_download/sequence/NCBI_genome_source/) reference genomes, converting the latter to that of the W303 strain as above. The ensuing analysis considered only uniquely-mappable (2) reads and the 4,238 ortholog pairs with a minimum of 200 uniquely-mappable (2) bases in both species and a maximum difference in length of 100 bp.
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| Submission date |
Feb 19, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Rachel B Brem |
| URL |
http://mcb.berkeley.edu/faculty/GEN/bremr.html
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| Organization name |
UC Berkeley
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| Department |
Molecular and Cell Biology
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| Street address |
304A Stanley Hall #3220
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720-3220 |
| Country |
USA |
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| Platform ID |
GPL10079 |
| Series (1) |
| GSE19837 |
Polygenic and directional regulatory evolution across pathways in Saccharomyces |
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| Relations |
| SRA |
SRX016663 |
| BioSample |
SAMN00008885 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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