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Sample GSM1484033 Query DataSets for GSM1484033
Status Public on Apr 23, 2015
Title wt_spb75_30C_2
Sample type SRA
 
Source name wt_spb75
Organism Schizosaccharomyces pombe
Characteristics strain: spb75
genotype/variation: wt
temperature: 30C
Treatment protocol no specific treatment
Growth protocol Strains grown in YES medium to OD600=0.5 at 30°C or 37°C
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 ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
 
Data processing All samples were sequenced (together with other libraries) on 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 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 each library. sRNA enriched regions were identified by peak calling with MACS algorithm.
Genome_build: S. pombe genome (May 8, 2009, http://www.sanger.ac.uk/Projects/S_pombe/)
Supplementary_files_format_and_content: tabular file with small RNA enrichment over MACS peaks, normalized for the length of the feature
 
Submission date Aug 22, 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)
GSE60638 Dicer and Hsp104 function in a negative feedback loop to confer epigenetic robustness [RNA_correlations]
GSE60640 Dicer and Hsp104 function in a negative feedback loop to confer epigenetic robustness
Relations
BioSample SAMN03002399
SRA SRX684876

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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