|
| Status |
Public on Dec 01, 2015 |
| Title |
mut-0h |
| Sample type |
SRA |
| |
|
| Source name |
Untreated cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
mutation: Prp4 kinase conditional mutant
time from induction: 0 h
treatment: Control sample
|
| Treatment protocol |
Cell were treated with the ATP analog 1NM-PP1 for 30 min, 60 min or left untreated
|
| Growth protocol |
Cells were gronw in standard EMM media to grow S. pombe
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using standard protocols for S pombe
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 |
Control sample (untreated cells)
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence by using Tagdust
Filtered reads were mapped to the reference genome by using Tophat splice mapper (v2.0.5) using the annotation defined in Ensembl database (version ASM294 v1.15)
Mapped reads were filtered removing the muli-mapped ones by using samtools
For each intron, the number of split and unsplit reads that mapped to the splice junction (defined as the three bases around the 5’ exon junction) were counted, and the base-2 logarithm of the ratio between the two values was calculated. This value is called the Relative Splicing Efficiency Index (RSEI). If the RSEI was positive, then more reads indicated spliced mRNA than unspliced pre-mRNA. On the other hand, a negative RSEI indicates more unspliced than spliced RNA.
Genome_build: ASM294v1
Supplementary_files_format_and_content: excel file a table with chromosome, start and end of each splicing site, gene name, strand, number of tags (that maps univocally) in each condition and corresponding log2 ratio. A pseudocount of 1 was added to both numerator and denominator,.
|
| |
|
| Submission date |
Nov 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jose Ayte |
| E-mail(s) |
jose.ayte@upf.edu
|
| Organization name |
Universitat Pompeu Fabra
|
| Lab |
Oxidative Stress and Cell Cycle Group
|
| Street address |
Doctor Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13988 |
| Series (1) |
| GSE75517 |
Prp4 Kinase Grants the License to Splice: Control of Weak Splice Sites during Spliceosome Activation |
|
| Relations |
| BioSample |
SAMN04302176 |
| SRA |
SRX1456335 |
