|
| Status |
Public on Mar 19, 2024 |
| Title |
WT_CaCl2_48_2 |
| Sample type |
SRA |
| |
|
| Source name |
haploid yeast
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell type: haploid yeast
genotype: MATa his3delta1 ura3delta0 leu2delta0 lys2delta0 ChrVI181901-182001::HYG-TEFp-GFP(Y66F)
treatment: 200mM CaCl2
time point: 48 hours
|
| Treatment protocol |
Yeast cells were grown in 200mM CaCl2 and diluted every 12 hours to maintain logarithmic growth. Samples were collected after 12, 48 and 72 hours of CaCl2 treatment for RNA isolation.
|
| Growth protocol |
All strains are in the BY4741 background and were grown in synthetic media with ammonium chloride as a nitrogen source.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was purified using an acid-phenol extraction protocol.
poyA enrichment and library construction were performed by BGI Americas
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Paired-end reads were aligned to Saccharomyces_cerevisiae.R64-1-1, with star_2.5.3a, annotated with Saccharomyces_cerevisiae.R64-1-1.90.gtf.
Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts. Differential expression (DE) analysis was performed with DESeq2. Within DE analysis, 'ashr' was used to create log2 Fold Change (LFC) shrinkage for each comparison. Significant DE genes (DEGs) were filtered with the criteria FDR < 0.05.
Assembly: Saccharomyces_cerevisiae.R64-1-1,
Supplementary files format and content: csv, raw count and TPM
|
| |
|
| Submission date |
Jan 30, 2024 |
| Last update date |
Mar 19, 2024 |
| Contact name |
Jennifer Benanti |
| E-mail(s) |
Jennifer.Benanti@umassmed.edu
|
| Phone |
508-856-1773
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Molecular, Cell and Cancer Biology
|
| Street address |
364 Plantation St., LRB 525
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL25927 |
| Series (2) |
| GSE254551 |
Identification of calcineurin-dependent gene expression changes in response to chronic CaCl2 stress |
| GSE254555 |
Identification of calcineurin-dependent gene expression changes in response to chronic stress |
|
| Relations |
| BioSample |
SAMN39671468 |
| SRA |
SRX23449082 |
