|
| Status |
Public on Jan 23, 2014 |
| Title |
wt_sRNA |
| Sample type |
SRA |
| |
|
| Source name |
sRNA from wild type S. pombe
|
| Organism |
Schizosaccharomyces pombe 972h- |
| Characteristics |
strain: 972h-
|
| Treatment protocol |
Liquid yeast cultures were grown in YES media at 30°C until mid-logarithmic phase.
|
| Growth protocol |
Yeast cultures were grown in YES media at 30°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were disrupted and total RNA was isolated by grinding frozen cell pellet using mortar and pestle in liquid nitrogen in the presence of Trizol (Invitrogen). The RNA was extracted using Trizol according to manufacturer's directions. 10-40 nt fraction was enriched using flashPAGE (Ambion).
The adapters (Small RNA Oligo Only, Illumina) were ligated sequentially using T4 RNA Ligase (Promega); each step was followed by purification by denaturing PAGE. The library was reverse-transcribed using Superscript II (Invitrogen) and amplified using Phusion Hot Start DNA Polymerase (Finnzymes).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
small RNA from wild type S. pombe cells
|
| Data processing |
The data were processed by searching the raw reads for adapter sequence and trimming it off, leaving only small RNA sequences (using custom written scripts).
The reads were mapped to S. pombe genome and mRNA sequences using WU-BLAST (Gish, W. 1996-2003).
The aligned reads were processed using custom written scripts, using genome feature annotation version 09-05-2011 (Sanger)
Genome_build: release 23-8-2007 (Sanger)
Supplementary_files_format_and_content: Spo_wt_sRNA.txt (Tab-delimited list of read sequence and count); RNAprofiling_sRNA_summary.txt (Tab-delimited list of genes and sRNA read counts per gene as well as log2 of strand specific mutant to wt ratio of RNA profiling values)
|
| |
|
| Submission date |
Jan 17, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Agata Smialowska |
| Organization name |
Karolinska Institute
|
| Department |
Biosciences and Nutrition
|
| Street address |
Halsovagen 7
|
| City |
Huddinge |
| ZIP/Postal code |
141 83 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL18187 |
| Series (2) |
| GSE54194 |
RNAi mediates post-transcriptional repression of gene expression in fission yeast Schizosaccharomyces pombe [Illumina Genome Analyzer] |
| GSE54195 |
RNAi mediates post-transcriptional repression of gene expression in fission yeast Schizosaccharomyces pombe |
|
| Relations |
| BioSample |
SAMN02593506 |
| SRA |
SRX444498 |
