|
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
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|
|
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
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|
|
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 |