|
| Status |
Public on Oct 01, 2021 |
| Title |
8h_34 degrees |
| Sample type |
SRA |
| |
|
| Source name |
pat1_as2 prp2-1 strain in meiosis I, at restrictive temperature (34 degrees)
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
mutation: prp2-1 (U2AF65)
time from induction: Synchronous meiosis, collected at the onset of meiosis I after 1 hour at restrictive temperature
|
| Growth protocol |
The strain was grown in Minimal Media at permissive temperature, arrested in G1 by nitrogen deprivation and the synchronous meiosis was chemically induced. At the onset of meiosis I, the culture was splitted in two, one was left at permisive temperature and the other half was shifted to restrictive temperature. Samples were collected after 1 hour.
|
| Extracted molecule |
polyA 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 |
| |
|
| 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 multi-mapped ones by using samtools
Introns were only taken into consideration if the sum of spliced and unspliced reads at the conditions 25°C and 34°C was bigger than 50. In order to avoid the division by 0, all read numbers that were equal to 0 were replaced with 1 read.
To determine the splicing efficiency, the ratio of spliced over unspliced reads at the conditions 25°C and 34°C was determined
Genome_build: ASM294v1
|
| |
|
| Submission date |
Mar 29, 2017 |
| Last update date |
Oct 01, 2021 |
| 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) |
| GSE97203 |
U2AF65Prp2 promotes intron definition by stabilizing U1 snRNP at the 5’ splice site |
|
| Relations |
| BioSample |
SAMN06652306 |
| SRA |
SRX2683716 |
