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Sample GSM2559620 Query DataSets for GSM2559620
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
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
BioSample SAMN06652306
SRA SRX2683716

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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