|
| Status |
Public on Aug 08, 2023 |
| Title |
Cdc55p-deficient yeast, 6 h in fermentative medium, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
yeast cell
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741
cell type: yeast cell
genotype: cdc55
treatment: 6 h in YPD20, statically incubated at 30 degree
|
| Treatment protocol |
Yeast cells were statically incubated at 30 degree for 6 h in YPD20 medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit in QIAcube Connect (QIAGEN).
rRNA was removed by riboPool (siTOOLs Biotech), and then total RNA sample was subjected to library construction using MGIEasy RNA Directional Library Prep Set (MGI Tech Co Ltd) according to the manufacturers' manuals.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
Sequenced reads were trimmed of adapters and sequencing quality lower than 20 (using cutadapt and sickle).
The RNAseq reads were aligned to S. cerevisiae S288C whole genome using Hisat2.
Read Per Kilobase of transcript per Million (RPKM) was calculated using featureCounts with gene level and converted to TPM (Transcripts Per Million) by in-house script.
Assembly: Saccharomyces cerevisiae S288C; GenBank assembly accession: GCA_000146045.2
Supplementary files format and content: Tab-delimited text file contains raw reads, RPKM values, and TPM values.
|
| |
|
| Submission date |
Dec 05, 2022 |
| Last update date |
Aug 08, 2023 |
| Contact name |
Daisuke Watanabe |
| E-mail(s) |
watanabe.daisuke@bs.naist.jp
|
| Organization name |
Nara Institute of Science and Technology
|
| Street address |
8916-5 Takayamacho
|
| City |
Ikoma |
| State/province |
Nara |
| ZIP/Postal code |
630-0192 |
| Country |
Japan |
| |
|
| Platform ID |
GPL30266 |
| Series (1) |
| GSE220072 |
Siginificance of Saccharomyces cerevisiae Cdc55p on gene expression at initial stage of alcoholic fermentation |
|
| Relations |
| BioSample |
SAMN32040539 |
| SRA |
SRX18491062 |
