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| Status |
Public on Jan 21, 2016 |
| Title |
xrn1_S288C_Ter_1 |
| Sample type |
SRA |
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| Source name |
Yeast cells
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype/variation: YAM6 xrn1D strain
background strain: S288C
replicate: 1
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using standard hot phenol procedure. rRNAs were depleted from total RNA using the RiboMinus Eukaryote System v2 (Life Technologies). Alternatively, total RNA was treated with Terminator 5'-Phosphate-Dependent Exonuclease (Epicentre) to digest all 5'-monophosphate-ended RNAs.
Strand-specific total RNA-Seq libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina), starting from 125 ng of rRNA-depleted RNA or Terminator-treated RNA . Paired-end sequencing (2x50 nt) of the libraries was performed on a HiSeq 2500 sequencer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Terminator-treated RNA
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| Data processing |
Reads were mapped to the S. cerevisiae S288C reference genome (retrieved from SGD) using the version 2.0.6 of TopHat, with a tolerance of 3 mismatches and a maximum size for introns of 5 Kb.
All bioinformatics analyses used reads uniquely mapped on the reference genome.
Tags densities were normalized on snoRNAs, that are insensitive to Xrn1.
Genome_build: S. cerevisiae S288C
Supplementary_files_format_and_content: A single tab-delimited text file including normalized tag densities (tag/nt) for each annotated feature (including XUT, SUT and CUT lncRNAs) in each sample
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| Submission date |
May 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Maxime Wery |
| E-mail(s) |
maxime.wery@curie.fr
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| Organization name |
Institut Curie
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| Department |
UMR3244
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| Lab |
Non-coding RNA, epigenetics and genome fluidity
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| Street address |
26 rue d'Ulm
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| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
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| Platform ID |
GPL17342 |
| Series (1) |
| GSE69384 |
Nonsense-Mediated Decay restricts lncRNAs levels in yeast unless blocked by double-stranded RNA structure |
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| Relations |
| BioSample |
SAMN03744281 |
| SRA |
SRX1043916 |
| 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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