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Sample GSM1250054 Query DataSets for GSM1250054
Status Public on Oct 25, 2013
Title YHL065 diploid hybrid
Sample type SRA
Source name wild-type hybrid
Organism Saccharomyces cerevisiae
Characteristics genotype: UWOPS05.217.3 x BC187 MATa/@ HO
growth medium: YPD
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
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.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
Description ASE_processed_data.txt
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
Submission date Oct 24, 2013
Last update date May 15, 2019
Contact name Rachel Brem
Organization name University of California, Berkeley
Street address 176 Stanley Hall # 3220
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
Platform ID GPL9377
Series (1)
GSE51645 Differential gene expression in Malaysian and Wine/European yeast isolates
BioSample SAMN02383523
SRA SRX367353

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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