|
| Status |
Public on Nov 07, 2021 |
| Title |
CLIB324_S1 |
| Sample type |
SRA |
| |
|
| Source name |
Liquid yeast cell culture
|
| Organism |
Saccharomyces paradoxus |
| Characteristics |
strain: wild isolate
isolate: CLIB324
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Three independent culture for each strain grown in YPD liquid medium with 2% glucose. OD600= 0.4 cells were collected with centrifugation and pellets were flash frozen with liquid nitrogen. Thre biological replicates for each strain
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each sample was isolated using Quick-RNA 96 Kit from Zymo Research (Cat. number: R1053)
After the QC procedures, Illumina TruSeq RNA library preparation kits were used according to the user manual.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Budding yeast
|
| Data processing |
After quality control and adapter removal, the STAR software package was used to map the reads against a pseudo reference genome of each strains, in which we replaced identified nucleotide changes in the S288c reference genome.
Read counts per gene were calculated using featureCounts. To filter out genes with low numbers of reads, we used filterByExpr function from the edgeR package. One biological replicates from DBVPG6044 and N44 were eliminated from analysis due to low sequencing read output.
The data contains expression set of 5,376 genes across replicates of wild isolates.
Genome_build: S288c
Supplementary_files_format_and_content: The raw and normalized counts table (.txt) contains expression set of 5,376 genes across replicates of each wild isolates.
|
| |
|
| Submission date |
Nov 05, 2021 |
| Last update date |
Nov 07, 2021 |
| Contact name |
Alaattin Kaya |
| E-mail(s) |
kayaa@vcu.edu
|
| Organization name |
Virginia Commonwealth University
|
| Department |
Biology
|
| Lab |
kayalab
|
| Street address |
1000 West Carry St, Room 126
|
| City |
Richmond |
| State/province |
VA |
| ZIP/Postal code |
23284 |
| Country |
USA |
| |
|
| Platform ID |
GPL30932 |
| Series (1) |
| GSE188294 |
Evolution of Natural Lifespan Variation and Molecular Strategies of Extended Lifespan |
|
| Relations |
| BioSample |
SAMN22933681 |
| SRA |
SRX13013766 |
