|
| Status |
Public on Jun 07, 2014 |
| Title |
ReutH16_F36 |
| Sample type |
SRA |
| |
|
| Source name |
R. eutropha H16, stationary phase
|
| Organism |
Cupriavidus necator H16 |
| Characteristics |
strain/background: H16
genotype/variation: wild-type
phase: stationary
cultivation: fructose for 36 h
strain: H16
|
| Treatment protocol |
The cells in 10 ml culture broth at 16, 26, and 36 h on fructose were harvested by centrifugation.
|
| Growth protocol |
R. eutropha wild H16 was cultivated in a 500 ml flask on a reciprocal shaker (115 strokes/min) at 30˚C with 100 ml of a nitrogen-limited mineral salts medium. A filter-sterilized solution of fructose was added to the medium at a final concentration of 0.5% (w/v).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the cells by using RNeasy Midi Kit (Qiagen), and treated with DNase I. 25-50 μg of total RNA was then subjected to repeated treatment using RiboMinus Transcriptome Isolation Kits (Yeast and Bacteria) (Invitrogen) for mRNA enrichment.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
mRNA-enriched
|
| Data processing |
Illumina Casava 1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome of R. eutropha using BWA with default paramters.
The alignments with mismatch or mapped to the five rRNA regions of R. eutropha H16 were discarded by using custom Perl scripts.
Reads Per Kilobase per Megabase of library size (RPKM) for each coding DNA sequence was calculated by using custom Perl scripts.
Genome_build: R. eutropha H16 Chromosome 1 (NC_008313.1), Chromosome 2 (NC_008314.1) and megaplasmid pHG1 (NC_005241.1).
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values and P-values.
|
| |
|
| Submission date |
Jun 07, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Toshiaki Fukui |
| E-mail(s) |
tfukui@bio.titech.ac.jp
|
| Organization name |
Tokyo Institute of Technology
|
| Department |
Department of Bioengineering
|
| Street address |
Nagatsuta 4259
|
| City |
Yokohama |
| ZIP/Postal code |
226-8501 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17263 |
| Series (1) |
| GSE47759 |
RNA-seq analysis of polyhydroxyalkanoate-producing Ralstonia eutropha H16 |
|
| Relations |
| BioSample |
SAMN02192881 |
| SRA |
SRX298049 |
