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Sample GSM2868420 Query DataSets for GSM2868420
Status Public on Jul 22, 2020
Title WT Aerobic rep 2
Sample type SRA
 
Source name whole cell
Organism Saccharomyces cerevisiae
Characteristics genotype: WT
stress: Aerobic
Treatment protocol Both BY4741 WT and BY4741 set4∆ strains were grown for 8 hours under hypoxia or 5.5 hours under aerobic conditions
Growth protocol S. cerevisiae (BY4741 WT, BY4741 set4∆ strains) Strains were grown to saturation overnight in SC media at 30 degrees C. Cells were back diluted to an OD600: 0.1 and grown to log phase at 30 degrees C in SC media for 8 hours under hypoxic conditions or 5.5 hours under aerobic conditions.
Extracted molecule total RNA
Extraction protocol Cells were harvested following 8 hours of growth under hypoxia or 5.5 hours of growth under aerobic conditions. At the indicated time points cells were pelleted and frozen using liquid nitrogen. Total RNA was isolated using phenol extraction protocol and treated with DNAse (Ambion).
An Illumina TruSeq Stranded kit was used to construct a cDNA library
RNA sequencing by Illumina HiSeq2500 next generation sequencer
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description WTRep2
Data processing FastQC v.0.11.3 was used to observe read quality
FastX v. 0.0.14 was used to trim data
Tophat2 v 2.1.0 was used to align reads to the genome with max-intron-length set to 560, min-intron-length set to 60, and strandedness set to "fr-firststrand".
HTSeq Count v. 0.6.1 was used to count reads aligning to genes, feature was set to "exon" and attribute was set to "gene id", stranded was set to "reverse" and intersection-nonempty was used
EdgeR v. 3.12.1 (using Bioconductor v 3.2) were used to normalize and perform DE analysis. The number of reads for the control and experimental groups were then compared to identify differentially expressed genes (false discovery raye of 1%)
Genome_build: Saccharomyces_cerevisiae.R64-1-1
Supplementary_files_format_and_content: BriggsGeneCounts_set4WT_forGEO.txt - raw abundance measurements
briggs_set1set4_rnaseq_CPM_WTset4_GEO.txt - CPM normalized abundance estimates
 
Submission date Nov 29, 2017
Last update date Jul 22, 2020
Contact name Nadia Marie Atallah
Organization name Purdue University
Department Center for Cancer Research
Street address 201 S. University St
City West Lafayette
State/province IN
ZIP/Postal code 47907
Country USA
 
Platform ID GPL17342
Series (1)
GSE107492 Transcriptional profiling of Saccharomyces cerevisiae WT and set4∆ strains during hypoxia
Relations
BioSample SAMN08109806
SRA SRX3429026

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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