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| Status |
Public on Oct 25, 2013 |
| Title |
YHL065 diploid hybrid |
| Sample type |
SRA |
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| Source name |
wild-type hybrid
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: UWOPS05.217.3 x BC187 MATa/@ HO
growth medium: YPD
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| Growth protocol |
Parental and hybrid strains were grown to mid-log phase (0.65-0.72 OD600) in yeast peptone dextrose (YPD) medium (Amberg et al, 2005) at 30° C
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells using the hot phenol method (Ausubel et al, 1995). Poly-A selection was done with magnetic beads, and genomic DNA was removed with Turbo Dnase I
Libraries were prepared as in Mortavazi et al, 2008. After random fragmentation, RNA was reverse-transcribed to double-stranded cDNA. Paired-end adapters were ligated onto cDNA, and size selection occurred through gel electrophoresis. Libraries were sequenced according to Illumina protocols for Genome Analyzer II and HiSeq 2000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
ASE_processed_data.txt
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| Data processing |
Paired-end read alignment with Bowtie 0.12.7
Read counts per gene determined with custom Python scripts
Counts normalized by library size between lanes and GC content within lanes using EDAseq package in R
Differential expression and p-value significance calculated using DESeq package in R
SGD amended with SNP calls for each respective strain
Supplementary_files_format_and_content: Tab-delimited text files contain the following data: gene name, raw counts per gene for each parental strain (DE_processed_data.txt) or each allele in hybrid strains (ASE_processed_data.txt), the mean normalized gene expression across all strains or alleles, the mean Wine/European expression, the mean Malaysian expression, the fold change of Wine/European : Malaysian expression, the log2 fold change, the p-value significance of the expression difference between Wine/European and Malaysian, the p-value corrected for multiple testing using Benjamini-Hochberg
Genome_build: n/a
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| Submission date |
Oct 24, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Rachel Brem |
| Organization name |
University of California, Berkeley
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| Street address |
176 Stanley Hall # 3220
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platform ID |
GPL9377 |
| Series (1) |
| GSE51645 |
Differential gene expression in Malaysian and Wine/European yeast isolates |
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| Relations |
| BioSample |
SAMN02383523 |
| SRA |
SRX367353 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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