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Sample GSM1585537 Query DataSets for GSM1585537
Status Public on May 20, 2015
Title rrp6Δ
Sample type SRA
 
Source name rRNA depleted RNA of rrp6Δ
Organism Schizosaccharomyces pombe
Characteristics strain: deletion strain: rrp6-delta (p74)
Treatment protocol NA
Growth protocol WT and gene deletion strains were grown in YEA at 30°C to OD 0.5~0.8. Temperature sensitive strains were grown in YEA at 23°C to OD 0.3~0.4 and then moved to 37°C and grown for 4 h to OD<0.8.
Extracted molecule total RNA
Extraction protocol RNA was isolated from either wildtype strains or deletion mutants using TRI Reagent (Sigma Aldrich) following the manufacturers instructions
Ribosomal RNAs were depleted from Turbo DNase-treated total RNAs using a Ribo-zero Magnetic Gold Kit (Epicentre). The cDNA libraries were prepared using NEBNext Ultra RNA Directional Library Prep Kit (NEB) according to the manufacturer’s instructions. The libraries were purified with Agencourt AMPure XP beads (Beckman Coulter) and assessed on a Bioanalyzer (Agilent). Subsequently, 2x100 bp paired-end sequencing was performed on an Illumina HiSeq 2000 sequencer at BGI Tech (Hong Kong).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description rRNA depleted RNA
Data processing fastq files were mapped using tophat-2.0.13
coverage was calculated for fw and rev strand separately
median coverage was calculated for all non-intron containing genes, and the median non-intron coding gene coverage was calculated for each dataset
datasets were normalized using the median non-intron containing gene coverage (set to 100)
Genome_build: Schizosaccharomyces_pombe_Ensembl_EF2
Supplementary_files_format_and_content: fw.BigWig and rev.BigWig files for each dataset describe the normalized RNA coverage at the fw/rev strand
 
Submission date Jan 15, 2015
Last update date May 15, 2019
Contact name Tamas Fischer
E-mail(s) tamas.fischer@bzh.uni-heidelberg.de
Phone +49 6221 544728
Organization name Biochemie Zentrum Heidelebrg
Department BZH
Lab AG Fischer
Street address Im Neuenheimer Feld 328
City Heidelberg
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL13988
Series (2)
GSE64991 The fission yeast MTREC complex targets CUTs and unspliced mRNAs to the nuclear exosome [RNA-Seq]
GSE64992 The fission yeast MTREC complex targets CUTs and unspliced mRNAs to the nuclear exosome
Relations
BioSample SAMN03284841
SRA SRX844148

Supplementary file Size Download File type/resource
GSM1585537_N.RNAseq.Sp.rrp6d.210214.fw.BigWig 23.0 Mb (ftp)(http) BIGWIG
GSM1585537_N.RNAseq.Sp.rrp6d.210214.rev.BigWig 23.4 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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