|
| Status |
Public on Apr 02, 2010 |
| Title |
Hybrid_cDNASeq_04 |
| Sample type |
SRA |
| |
|
| Source name |
Hybrid_cDNASeq_04
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741xRM11-1alpha
|
| Treatment protocol |
Each of the replicated subcultures of BYxRM hybrid and BY+RM co-culture harvested at OD600=1.0 was used to extract total RNA by the hot acid phenol method (Kohrer and Domdey 1991)
|
| Growth protocol |
Overnight subcultures were used to prepare four technical replicates each of BYxRM hybrid (WL201) cultures and BY+RM co-cultures with starting OD600 at 0.1 and harvested overnight subcultures were used to prepare four technical replicates each of hybrid (WL201) cultures and BY+RM co-cultures with starting OD600 at 0.1 and harvested when cell density reached OD600=1.0 at 30'C, 250rpm
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The hybrid and co-culture mRNA was purified on Invitrogen's oligo-dT Dynabeads according to the manufacturer's protocol. Subsequent reverse transcription was carried out with oligo-dT primers and the Superscript II
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
a/alpha diploid
|
| Data processing |
The sequence reads of each sample were mapped on each reference yeast genome (the BY reference genome was downloaded from the Saccharomyces Genome Database ftp://ftp.yeastgenome.org/yeast/ (Apr. 2008), and the RM reference genome was downloaded from the Saccharomyces cerevisiae RM11-1a Database http://www.broadinstitute.org/annotation/genome/saccharomyces_cerevisiae/Home.html) and all reads mapping with two or fewer mismatches were retained . In addition, 4442 reliable orthologous gene pairs with single nucleotide polymorphism (SNP) sites were identified between the two strains. The sequence reads mapped on the SNPs for each of the gene pairs were counted and then allele-specific expression can be measured between BY and RM.
|
| |
|
| Submission date |
Mar 11, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Li-Ching Hsieh |
| Organization name |
National Chung Hsing University
|
| Department |
Graduate Institute of Genomics and Bioinformatics
|
| Lab |
Hsieh Lab
|
| Street address |
145 Xingda Rd.
|
| City |
Taichung |
| ZIP/Postal code |
402 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL9134 |
| Series (1) |
| GSE20749 |
Natural selection on cis and trans regulation in yeasts |
|
| Relations |
| SRA |
SRX018755 |
| BioSample |
SAMN00010895 |
