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Sample GSM5677095 Query DataSets for GSM5677095
Status Public on Nov 07, 2021
Title DBVPG4650_S1
Sample type SRA
 
Source name Liquid yeast cell culture
Organism Saccharomyces paradoxus
Characteristics strain: wild isolate
isolate: DBVPG4650
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 SAMN22933656
SRA SRX13013784

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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