|
| Status |
Public on May 20, 2024 |
| Title |
WT_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
yeast
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
cell type: yeast
genotype: WT (972)
treatment: untreated
|
| Growth protocol |
WT (972), saf5 and cwf12 strain were grown in YE5S media at 30ºC at OD600 of 0.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot phenol extraction
TrueSeq Stranded mRNA sample Prep kit v2 following manufacterer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Quality controls for fastq.gz files using fastq.gzC
Trim of low quality read bases from fastq.gz files as well as removal of adapters and other contaminants using Trimmomatic
Alignment againts the Schizosaccharomyces pombe ASM294v2 genone referenceusing STAR
Confirmation that no coverage biases are present in the aligned data according to genomic reference file using QualiMap2
Read count overlapping Schizosaccharomyces pombe ASM294v2 genomic features using htseq-count
Test for differentially expressed features between conditions using DESeq2
Assembly: Schizosaccharomyces pombe ASM294v2
Supplementary files format and content: tab-separated .txt table of raw counts for all the samples
|
| |
|
| Submission date |
Sep 05, 2023 |
| Last update date |
May 20, 2024 |
| Contact name |
Montserrat Vega |
| E-mail(s) |
montserrat.vega@upf.edu
|
| Organization name |
Universitat Pompeu Fabra
|
| Department |
MELIS
|
| Lab |
OSCCG
|
| Street address |
C/ Dr. Aiguader 88, lab 383
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL30658 |
| Series (1) |
| GSE242312 |
A systematic screen identifies Saf5 as a link between splicing and transcription in fission yeast |
|
| Relations |
| BioSample |
SAMN37283546 |
| SRA |
SRX21635531 |
