|
| Status |
Public on Sep 01, 2012 |
| Title |
wild-type (1) |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells, WT
|
| Organism |
Rhodopseudomonas palustris CGA009 |
| Characteristics |
strain/background: CGA009
genotype: wild-type
strain: CGA009
|
| Growth protocol |
Cells were grown anaerobically in light in photosynthetic medium plus 10 mM succinate at 30C until an OD660 = 0.5 was reached; cells were pelleted, flash frozen, and stored at -80C until processed for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified from frozen cell pellets using a miRNeasy Mini Kit following the manufacturer's instructions. RNA was treated with TURBO DNase and purified with an RNeasy MinElute Cleanup Kit. The construction of the cDNA library was performed as described previously (Armour et. al., 2009 (PMID 19668204)). Briefly, first-strand cDNA synthesis was carried out using first-strand NSR (Not-So-random) primer mix and SuperScript III enzyme. RNA template was then removed by RNase H. Second-strand synthesis was carried out with exo- Klenow fragment and second-strand NSR primer mix. After PCR amplification, double-stranded DNA was purified using a QIAquick PCR Purification Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
YO1
cDNA from RNA.
|
| Data processing |
Xpression was used for filtering and trimming reads.
Xpression called BWA to align reads against the R. palustris strain CGA009 genome (BX571963.1).
Xpresssion was used for quantifying, normalizing and visualizing read counts.
DESeq was used for identifying differentially expressed genes.
Genome_build: gi|39748133
Supplementary_files_format_and_content: Bed files were generated for each sample.
|
| |
|
| Submission date |
Jun 29, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Somsak Phattarasukol |
| Organization name |
University of Washington
|
| Department |
Microbiology
|
| Lab |
Harwood
|
| Street address |
1705 NE Pacific St., HSC K-327
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
|
| Platform ID |
GPL15760 |
| Series (1) |
| GSE39025 |
Identification of a p-coumarate degradation regulon in Rhodopseudomonas palustris using Xpression, an integrated tool for prokaryotic RNA-seq data processing |
|
| Relations |
| SRA |
SRX157442 |
| BioSample |
SAMN01085310 |
