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Sample GSM1264159 Query DataSets for GSM1264159
Status Public on Mar 13, 2014
Title S2A 2
Sample type SRA
Source name S. pombe cells
Organism Schizosaccharomyces pombe
Characteristics strain: rpb1CTD-S2A
genetic markers: h+ ade6 ura4-D18 leu1–32
Growth protocol Two biological replicates of the WT, Y1F, S2A, T4A, S7A,Y1F-S7A, S2A-S7A and T4A-S7A cultures were grown in YES (yeast extracts plus supplements) media at 30°C till they reached OD600 0.4 -0.7.
Extracted molecule polyA RNA
Extraction protocol Cells were harvested and RNA was isolated using the Qiagen RNeasy kit. RNA quality was assessed on a Bioanalyzer instrument (Agilent) and 1µg of total RNA was used to prepare polyA+ RNA using the Illumina TruSeq RNA sample kit .
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded total RNA Sample Prep Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled (8 samples per lane) for paired-end sequencing performed using an Illumina HiSeq 2000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description S2A-2 (Name in expression table)
Data processing Paired-end reads of length 51 bases (each part) originating from each sample were aligned using Bowtie 0.12.7 to the S. pombe genome sequence (Ensembl S. pombe, Build EF1) as well as to its corresponding exon-exon junctions database (only thesecond part of the paired-end reads was considered). Up to 3 mismatches were allowed. Reads that matched multiple loci were removed from further analysis and the resultant alignment files were processed to generate ‘pile-ups’ against each chromosome.
Searches were performed against the genome sequence combined with a dataset of known exon-exon junctions as defined by Ensembl S. pombe release-13. To ensure that a 51-base read mapped to a splice junction, only the last 45 bases of the first exon and the first 45 bases of the second exon were considered (if the exon length exceeded 45 nucleotides). In this way, reads that overlapped a junction by less than 6 nucleotides were excluded. Reads that matched to more than one junction or elsewhere in the genome were also discarded.
Genome_build: Ensembl S. pombe, Build EF1, version 58.1a
Supplementary_files_format_and_content: Expression table and RPKM summary for all samples tab-delimited
Submission date Nov 14, 2013
Last update date May 15, 2019
Contact name Danny Asher Bitton
Phone +44(0)203-108-1604
Organization name University College London
Department Department of Genetics, Evolution & Environment
Lab Genome Regulation/Bähler Lab
Street address Darwin Building, Gower Street
City London
ZIP/Postal code WC1 6BT
Country United Kingdom
Platform ID GPL13988
Series (1)
GSE52370 Individual letters of the RNA polymerase II CTD code govern distinct gene expression programs in fission yeast
BioSample SAMN02402423
SRA SRX377477

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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