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Sample GSM1958430 Query DataSets for GSM1958430
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
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
BioSample SAMN04302176
SRA SRX1456335

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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