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Status |
Public on Jul 31, 2024 |
Title |
NKSW7-1 rep2 |
Sample type |
SRA |
|
|
Source name |
yeast cells
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
tissue: yeast cells genotype: NKSW7-1 strain (PHO13::XYL1,XYL2,XYL3 ; ALD6::XYL1,XYL2,XYL3 ; HXT1-7 :: AtSWEET7, GAL2 :: AtSWEET7)
|
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
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|
|
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
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|
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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 |
SAMN36697531 |
SRA |
SRX21142193 |