|
| Status |
Public on Jul 31, 2024 |
| Title |
CT2-control rep3 |
| Sample type |
SRA |
| |
|
| Source name |
yeast cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
tissue: yeast cells
genotype: CT2 strain (PHO13::XYL1,XYL2,XYL3 ALD6::XYL1,XYL2,XYL3)
|
| Growth protocol |
cells were grown in YP 5 g/L glucose media and harvested in mid exponential phase
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Quick-RNA™ Fungal/Bacterial Kits according to manufacturer protocol
The RNAseq libraries were prepared with Kapa Hyper Stranded mRNA library kit (Roche) . Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adapters and low-quality reads were trimmed using Trimmomatic
Trimmed reads were mapped onto S. cerevisiae S288C reference genome (RefSeq assembly accession: GCF_000146045.2) using STAR version 2.6.1b
Read counts for each gene were calculated using featureCounts from the Subread package, version 1.5.2
Differential expression analysis was performed in R using edgeR and limma
Glimma and gplots were used for graphical representation of expression data
Assembly: S. cerevisiae S288C reference genome GCF_000146045.2
Supplementary files format and content: tab delitmeted txt file containing raw counts
|
| |
|
| Submission date |
Jul 24, 2023 |
| Last update date |
Jul 31, 2024 |
| Contact name |
Nurzhan Kuanyshev |
| E-mail(s) |
nureke1286@gmail.com
|
| Organization name |
University of Illinois at Urbana Champaign
|
| Department |
CABBI
|
| Street address |
1206 W Gregory Dr
|
| City |
Urbana |
| State/province |
Illinois |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL27812 |
| Series (1) |
| GSE238127 |
All you can eat yeast: substitution of major hexose transporters by AtSWEET7 in Saccharomyces cerevisiae enables simultaneous utilization of multiple sugars |
|
| Relations |
| BioSample |
SAMN36697533 |
| SRA |
SRX21142191 |
