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Sample GSM8045787 Query DataSets for GSM8045787
Status Public on Mar 19, 2024
Title WT_CaCl2_12_1
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: 12 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 SAMN39671472
SRA SRX23449078

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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