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Sample GSM1429720 Query DataSets for GSM1429720
Status Public on Mar 25, 2015
Title Leo1D_spb1955_1
Sample type SRA
 
Source name Leo1D_spb1955_1
Organism Schizosaccharomyces pombe
Characteristics strain: spb1955
genotype/variation: Leo1Δ, ade6-hp+
Growth protocol Strains grown at 30 degress in YES medium to OD600=0.5
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® TruSeq small RNA preparation protocol (Cat.# RS-930-1012).
 
Library strategy miRNA-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.
Alignments to the S. pombe genome (May 8, 2009, http://www.sanger.ac.uk/Projects/S_pombe/) were performed for the minus strand by the software bowtie (version 0.9.9.1) ( Langmead et al., 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches. Alignments were normalized for the size of the each library, transformed into log2 scale and corrected with a pseudocount of 3. Annotations were used as described in Woolcock et al., Genes Devc 2012, PMID: 22431512
Genomic read coverage plots were made created separately for the plus (wiggle files with _p_) and minus (wiggle files with _m_) strand, transformed into log2 scale and normalized for the size of each library based on weights of the alignments
Genome_build: May 8, 2009, http://www.sanger.ac.uk/Projects/S_pombe/
Supplementary_files_format_and_content: wiggle files containing log2 scaled and normalized coverage values
 
Submission date Jul 07, 2014
Last update date May 15, 2019
Contact name Tim Roloff
E-mail(s) tim.roloff@fmi.ch
Organization name FMI
Department Functional Genomics
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platform ID GPL13988
Series (2)
GSE59170 RNA expression profiling for Paf1 complex mutant strains [miRNA]
GSE59171 RNA expression profiling for Paf1 complex mutant strains
Relations
BioSample SAMN02904623
SRA SRX647469

Supplementary file Size Download File type/resource
GSM1429720_spb1955_m_log_libnorm.wig.gz 827.2 Kb (ftp)(http) WIG
GSM1429720_spb1955_p_log_libnorm.wig.gz 803.3 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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