|
| Status |
Public on Jan 16, 2023 |
| Title |
BT0510, Oxidative stress - alcohol stress, biological replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
BT0510
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell line: BT0510
cell type: WT
treatment: Oxidative stress followed by ethanol stress
|
| Treatment protocol |
For osmotic stress, cells were incubated in liquid SC containing 1 M sorbitol for 30 minutes at 28ºC. Cells were subjected to oxidative stress by incubating them in SC containing 0.6mM hydrogen peroxide for 30 min. Glucose withdrawal was performed by transferring cells in SC + 2% glucose to SC + 0.05% glucose for 30 minutes. After each stress, cells were collected, washed with deionized water and reinoculated in SC supplemented with 8% (v/v) ethanol for 30 minutes at 28ºC at 160 rpm.
|
| Growth protocol |
Yeast cells were grown at 30 °C with aeration in liquid Synthetic Complete medium (SC) (yeast nitrogen base without amino acids, drop-out mix, 2% Glucose) to exponential growth phase (OD600nm = 1.0) before being exposed to sequential stresses.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from three biological replicates for each treatment was extracted using the Qiagen RNeasy Mini kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.
Poly-A tailed RNA was captured, and reverse transcribed to complementary DNA (cDNA), which was used for library preparation by the Stranded Total RNA Prep (Illumina, USA) following the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
G368-42
|
| Data processing |
Reads were aligned to the S288C reference genome with hisat2 using the --no-mixed --no-discordant parametrs
FPKM values for each sample and its associated control sample are provided in the gene_exp.diff file with column q1 providing the sample FPKM value and column q2 the control FPKM value
For the analysis presented in Figure 1, each value represents the log2 ratio of the FPKM value for that sample relative to the average of the values for all nine samples for that gene across all nine samples in that particular experiment
Assembly: Saccharomyces cerevisiae S288C R64-1-1
|
| |
|
| Submission date |
Dec 22, 2022 |
| Last update date |
Jan 16, 2023 |
| Contact name |
James R Broach |
| E-mail(s) |
jbroach@hmc.psu.edu
|
| Organization name |
Pennsylvania State University College of Medicine
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
700 HMC Crescent Rd
|
| City |
Hershey |
| State/province |
PA |
| ZIP/Postal code |
17033 |
| Country |
USA |
| |
|
| Platform ID |
GPL27812 |
| Series (1) |
| GSE221570 |
Transcriptional Response of Multi-stress Tolerant Saccharomyces cerevisiae to Sequential Stress |
|
| Relations |
| BioSample |
SAMN32367105 |
| SRA |
SRX18822534 |
