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Sample GSM1479700 Query DataSets for GSM1479700
Status Public on Apr 23, 2015
Title wt_spb75_37C_7d
Sample type SRA
Source name wt_spb75
Organism Schizosaccharomyces pombe
Characteristics strain: spb75
genotype/variation: wt
temperature: 37C
time: 7d
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, were performed by the software bowtie (version ( 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.
Wiggle files were generated with window size 100, normalized to the library size and transformed into log2 scale.
Genome_build: S. pombe genome (May 8, 2009,
Supplementary_files_format_and_content: wig file for sequencing coverage with fixed step 100bp windows
Submission date Aug 14, 2014
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)
GSE60429 Dicer and Hsp104 function in a negative feedback loop to confer epigenetic robustness [RNA_profiles]
GSE60640 Dicer and Hsp104 function in a negative feedback loop to confer epigenetic robustness
BioSample SAMN02990654
SRA SRX681490

Supplementary file Size Download File type/resource
GSM1479700_wt_37degrees_7d.wig.gz 387.7 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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