|
| Status |
Public on Aug 11, 2015 |
| Title |
xrn1 |
| Sample type |
SRA |
| |
|
| Source name |
Yeast cells_xrn1
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YAM2271
genotype: xrn1-delta
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small-RNA libraries were constructed according to the Small RNA Sample Preparation Guide (Illumina) using 10-40 nt small RNAs purified from total RNA on 15% TBE-urea PAGE or with a flashPAGE Fractionator (Ambion). Size selection was validated by qualitative analysis of a sample of the purified small RNA fraction on a Small RNA chip in a 2100 bioanalyzer (Agilent).
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Adapter sequences were removed using cutadapt.
14-40 nt reads were mapped to the S. cerevisiae reference genome (retrieved from SGD) using the version 0.12.7 of Bowtie, with a tolerance of 3 mismatches.
Tag densities were obtained using uniquely mapped 19-23 nt reads, after normalization on the total number of 19-23 nt reads that uniquely mapped on ORFs.
Genome_build: S. cerevisiae S288C
Supplementary_files_format_and_content: text file with normalized tag densities
|
| |
|
| Submission date |
Dec 11, 2014 |
| 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 |
GPL13272 |
| Series (1) |
| GSE64090 |
Mapping of dsRNA in yeast using reconstituted RNAi pathway |
|
| Relations |
| BioSample |
SAMN03262815 |
| SRA |
SRX806612 |
