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Sample GSM1051312 Query DataSets for GSM1051312
Status Public on Jul 20, 2013
Title dcr1 delta
Sample type SRA
Source name dcr1 delta
Organism Schizosaccharomyces pombe
Characteristics strain: spb361
genotype: dcr1 delta
Growth protocol Yeast strains were grown at 30°C in YES
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from exponentially growing cells using the hot phenol method (Leeds, 1991). The RNA was fractionated using RNeasy Midi columns (Qiagen) following the „RNA cleanup protocol“ provided by the manufacturer. The flow-through fraction was precipitated („small RNA“ fraction). 25 μg of the "small RNA" fraction were separated on a 17.5% PAGE and the 18 – 28 nt population was purified.
The isolated small RNA populations were prepared for sequencing using the Illumina® TruSeqTM small RNA preparation protocol (Cat.# RS-930-1012).
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
Data processing All samples were sequenced (together with other libraries) on one lane of an HiSeq 2000 instrument. Individual reads were assigned to their sample based on the TruSeq barcode. Illumina software Casava v 1.8 was used.
The 3' adapter was removed by aligning it to the read allowing one or two mismatches in prefix alignments of at least 7 or 10 bases respectively. Low complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). All the reads that were shorter than 14 nucleotides were removed.
Genome_build: n/a
Supplementary_files_format_and_content: Tabular, Columns: unique id, sequence, sequence count, original id from raw files if sequence is unique, or from first occurence in the raw data file
Submission date Dec 11, 2012
Last update date May 15, 2019
Contact name Tim Roloff
Organization name FMI
Department Functional Genomics
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
Platform ID GPL13988
Series (2)
GSE42849 Small RNA expression in swi6 mutants or dcr1 delta fission yeast Schizosaccharomyces pombe
GSE42850 Heterochromatin state in fission yeast Schizosaccharomyces pombe
SRA SRX209527
BioSample SAMN01830795

Supplementary file Size Download File type/resource 47.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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