|
| Status |
Public on Jun 22, 2020 |
| Title |
WT + Ramycin rep1 [rapa11] |
| Sample type |
SRA |
| |
|
| Source name |
WT + Ramycin
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain background: BY4741
genotype/variation: wild type
|
| Treatment protocol |
In case of rapamycin-treated cells, cultures were incubated overnight in YPD containing 50ng/ml of rapamycin until OD600 of about 0.8.
|
| Growth protocol |
Yeast strains were cultured in YPD liquid medium at 30ºC unless otherwise specified, until OD600 of about 0.8.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sequencing cDNA libraries were performed using the QuantSeq 3' mRNA-Seq Library Prep Kit form Illumina following the manufacturer instructions; as above, they were sequenced in an Illumina HiSeq 2000 instruments.
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 |
| |
|
| Description |
none
|
| Data processing |
Input DNAs were sequenced in an Illumina HiSeq 2000 instrument
The quality metrics of the Fastq sequencing datasets were obtained with FastQC and inspected visually
Sequencing adapters were removed from raw reads with Fastx Clipper
The resulting high-quality sequences were mapped to the S. cerevisiae S288c genome (SGD R64) with Hisat2
Resulting SAM, previously obtained from the BAM, were analyzed in the R/Bioconductor software, based on an advanced version of the DESeq package, DESeq2
Supplementary_files_format_and_content: abundance measurements
|
| |
|
| Submission date |
May 17, 2019 |
| Last update date |
Jun 22, 2020 |
| Contact name |
Francisco Navarro |
| E-mail(s) |
fngomez@ujaen.es
|
| Phone |
0034953212771
|
| Organization name |
Universidad de Jaén
|
| Department |
Experimental Biology
|
| Lab |
Genetic
|
| Street address |
Campus Las Lagunillas s/n.
|
| City |
Jaén |
| State/province |
Jaén |
| ZIP/Postal code |
23071 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13821 |
| Series (2) |
| GSE131389 |
Global analyisis to study the bud27∆ and WT treated with rapamycin regarding to WT [RNA-seq] |
| GSE131390 |
Prefoldin-like Bud27 influences the transcription of ribosomal components and ribosome biogenesis in Saccharomyces cerevisiae |
|
| Relations |
| BioSample |
SAMN11668093 |
| SRA |
SRX5854411 |
