|
| Status |
Public on Oct 10, 2015 |
| Title |
D8B rep2 |
| Sample type |
SRA |
| |
|
| Source name |
thiol peroxidase null yeast strain
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: S288c
genotype/variation: MATa, his3 leu2 met15 ura3 delta-tsa1:KAN, delta-tsa2:LEU2,delta-dot5:MET15, delta-ahp1:HIS3, delta-prx1:URA3, delta-gpx2:HYG, delta-gpx1:URA3, delta-gpx3:KAN,delta-srx1:NAT
|
| Growth protocol |
yeast extract-peptone-dextrose (YPD) medium
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Frozen aliquots were thawed and lysed in 400 μL of lysis buffer (mRNA DIRECT kit; Invitrogen). A 250-μL aliquot of magnetic beads and two rounds of purification were implemented according to the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
FASTQ files were aligned to the yeast genome, ensembl build R64-1-1 downloaded from the Illumina iGenome resource at http://goo.gl/LspLBZ, using Bowtie2 v2.1.0 [PMID 22388286] and the spliced-read mapper TopHat (v2.0.9) [PMID 23618408] and reference gene annotations to guide the alignment (-G argument in TopHat).
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using a Cufflinks v2.1.1 [PMID 22383036], with default parameters.
Genome_build: ensembl R64-1-1 (GCA_000146045.2)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample (abundance measurements).
|
| |
|
| Submission date |
Jun 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Inge Seim |
| Organization name |
Queensland University of Technology
|
| Lab |
Comparative and Endocrine Biology Laboratory
|
| Street address |
37 Kent St
|
| City |
Woolloongabba |
| State/province |
Queensland |
| ZIP/Postal code |
4173 |
| Country |
Australia |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE70036 |
Adaptive aneuploidy protects against thiol peroxidase deficiency by increasing respiration via key mitochondrial proteins |
|
| Relations |
| BioSample |
SAMN03782981 |
| SRA |
SRX1066427 |
