|
| Status |
Public on Mar 20, 2018 |
| Title |
rrp6_1 |
| Sample type |
SRA |
| |
|
| Source name |
Yeast cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: rrp6 delta strain
replicate: Biological replicate 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using standard hot phenol procedure. ERCC RNA Spike-In (2 µl of 1:100 dilution; Ambion) was added to 1 µg of total RNA, then rRNAs were depleted using the RiboMinus Eukaryote System v2 (Life Technologies).
Strand-specific total RNA-Seq libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina). Paired-end sequencing (2x50 nt) of the libraries was performed on a HiSeq 2500 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
rRNA-depleted RNA
|
| Data processing |
Reads were mapped to the S. pombe reference genome using version 2.0.6 of TopHat, with a tolerance of 3 mismatches and a maximum size for introns 5 Kb.
All subsequent bioinformatics analyses used reads uniquely mapped on the reference genome.
Tags densities were normalized on the ERCC Spike-In signals
Supplementary_files_format_and_content: A single tab-delimited text file including normalized tag densities (tag/nt) for each annotated feature (including CUTs) in each sample
|
| |
|
| Submission date |
Oct 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Maxime Wery |
| E-mail(s) |
maxime.wery@curie.fr
|
| Organization name |
Institut Curie
|
| Department |
UMR3244
|
| Lab |
Non-coding RNA, epigenetics and genome fluidity
|
| Street address |
26 rue d'Ulm
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL17225 |
| Series (1) |
| GSE104713 |
Total RNA-Seq in WT and rrp6-delta strains of S. pombe |
|
| Relations |
| BioSample |
SAMN07757741 |
| SRA |
SRX3257839 |
