|
| Status |
Public on Oct 23, 2023 |
| Title |
WT_treated_rep2 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
WT (972)
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: WT (972)
treatment: 30 min 1mM H2O2
|
| Treatment protocol |
1mM H2O2 during 30 minutes
|
| Growth protocol |
WT (972) and top1 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 |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Quality controls for FASTQ files using FastQC
Trim of low quality read bases from FASTQ files as well as removal of adapters and other contaminants using Trimmomatic
Alignment againts the Schizosaccharomyces pombe ASM294v2 genone reference using 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 DEseq2 Normalized counts for all the samples
|
| |
|
| Submission date |
Mar 12, 2023 |
| Last update date |
Oct 23, 2023 |
| 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 |
GPL13988 |
| Series (2) |
| GSE227183 |
Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery [RNA-seq] |
| GSE227184 |
Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery. |
|
| Relations |
| BioSample |
SAMN33730842 |
| SRA |
SRX19645459 |
