|
| Status |
Public on Feb 08, 2022 |
| Title |
sin3 |
| Sample type |
SRA |
| |
|
| Source name |
Early-log phase cells grown on YP medium containing 200 g/l glucose at 40ºC
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: ScY01a (sin3-delta)
genotype: SIN3 deletion strain
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sample were grown on YP medium containing 200 g/l glucose at 40ºC at 200 rpm for 10 h to the early-log phase, and harvested in Falcon tubes precooled in liquid N2 by centrifuging for 5 minutes at 4000 rpm (3220 × g). The supernatant was discarded, and the pellet was stored at −80°C until further use. Total RNA extraction, library construction and sequencing were conducted by GENEWIZ Inc. (Suzhou, Jiangsu, China).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Transcriptome profiles of all sequenced strains.xlsx
Differential gene expression_sin3 vs. ScY01a.xlsx
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to reference genome using Bowtie 1.2.0 with default parametres
Abundance measurements by RSEM
Differential gene expression by R package DESeq2, a p-value cutoff of 0.05 or less and an absolute fold-change threshold of 2.0 or greater.
Genome_build: R64
Supplementary_files_format_and_content: Transcriptome profiles of all sequenced strains.xlsx: Windows Excel file include abundance for each sample
Supplementary_files_format_and_content: Differential gene expression_ric1 vs. ScY01a.xlsx: Windows Excel file include different expression gene list and fold change of two samples
Supplementary_files_format_and_content: Differential gene expression_srb2 vs. ScY01a.xlsx: Windows Excel file include different expression gene list and fold change of two samples
Supplementary_files_format_and_content: Differential gene expression_sin3 vs. ScY01a.xlsx: Windows Excel file include different expression gene list and fold change of two samples
Supplementary_files_format_and_content: Differential gene expression_mig1 vs. ScY01a.xlsx: Windows Excel file include different expression gene list and fold change of two samples
|
| |
|
| Submission date |
Sep 27, 2017 |
| Last update date |
Feb 08, 2022 |
| Contact name |
Qinhong Wang |
| E-mail(s) |
wang_qh@tib.cas.cn
|
| Organization name |
Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences
|
| Lab |
Wang lab
|
| Street address |
32 West 7th Avenue, Tianjin Airport Economic Area
|
| City |
Tianjin |
| ZIP/Postal code |
300308 |
| Country |
China |
| |
|
| Platform ID |
GPL21656 |
| Series (1) |
| GSE104356 |
Transcriptome reprogramming of key transcription factor deletion strains of Saccharomyces cerevisiae compared with the wild type strain by RNA-Seq |
|
| Relations |
| BioSample |
SAMN07711222 |
| SRA |
SRX3223643 |
