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| Status |
Public on Apr 23, 2015 |
| Title |
dcr_delta_spb309 |
| Sample type |
SRA |
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| Source name |
dcr_delta_spb309
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| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: spb309
genotype/variation: dcr delta
temperature: 30C
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| Treatment protocol |
no specific treatment
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| Growth protocol |
Strains grown in YES medium to OD600=0.5 at 30°C or 37°C
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| 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).
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| 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
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| Submission date |
Aug 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Tim Roloff |
| E-mail(s) |
tim.roloff@fmi.ch
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| Organization name |
FMI
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| Department |
Functional Genomics
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| Street address |
Maulbeerstrasse 66
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| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
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| 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 |
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| Relations |
| BioSample |
SAMN03002396 |
| SRA |
SRX684873 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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