|
| Status |
Public on Jul 20, 2013 |
| Title |
NLS-swi6-KR25A |
| Sample type |
SRA |
| |
|
| Source name |
NLS-swi6-KR25A
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: spb1227
genotype: NLS-swi6-KR25A
|
| 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 |
| 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) |
| GSE42849 |
Small RNA expression in swi6 mutants or dcr1 delta fission yeast Schizosaccharomyces pombe |
| GSE42850 |
Heterochromatin state in fission yeast Schizosaccharomyces pombe |
|
| Relations |
| SRA |
SRX209526 |
| BioSample |
SAMN01830794 |
