|
| Status |
Public on May 31, 2014 |
| Title |
Pabyssi_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
cells
|
| Organism |
Pyrococcus abyssi |
| Characteristics |
strain: GE5
|
| Treatment protocol |
After two overnight transfers, cells were diluted to 2 × 106 cells/mL. After an initial growth of 3 h, samples (10 mL) were taken every 1.5 h until cells reach the stationary phase (11 h of growth). Samples were quickly cooled down in liquid nitrogen, spinned, and the pellets were frozen at −80°C
|
| Growth protocol |
Pyrococcus abyssi GE5 was grown anaerobically in ASW-YT rich medium, containing artificial seawater, yeast extract and tryptone40 at 92 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using the TRIzol method (Invitrogen). A pool of equal amounts of each sample was checked for integrity by 2100 Bioanalyzer (Agilent Technologies Inc.) and treated to enrich in primary transcripts using a 5'-phosphate-dependent exonuclease (Terminator, Epicenter). RNA samples were subsequently purified and concentrated using the RNA Clean-Up and Concentration Kit (Norgen Biotek Corp).
The strand-specific RNA-seq template library was prepared starting from a pool of total samples (50 ng) following the directional mRNA-seq library preparation protocol provided by Illumina Inc.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Mapping performed with bowtie.0.12.7 (parameters : -q -m 1)
ncRNA were identified and classified into long five_prime_UTR (utr5), small_regulatory_ncRNA (sRNA), or antisense_RNA (asRNA) using the detrprok_wf.1 (Galaxy Tool Shed)
Genome_build: NC_000868.2
Supplementary_files_format_and_content: gff files include overlapping read count
|
| |
|
| Submission date |
May 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Claire Toffano-Nioche |
| E-mail(s) |
[email protected]
|
| Organization name |
CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay
|
| Department |
UFR des Sciences
|
| Lab |
Institute for Integrative Biology of the Cell (I2BC)
|
| Street address |
Avenue de la Terrasse, b. 21
|
| City |
Gif-sur-Yvette |
| ZIP/Postal code |
91198 |
| Country |
France |
| |
|
| Platform ID |
GPL18745 |
| Series (1) |
| GSE58131 |
RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi. |
|
| Relations |
| BioSample |
SAMN02808713 |
| SRA |
SRX556571 |
