|
| Status |
Public on Dec 20, 2013 |
| Title |
Shew12222010.4 |
| Sample type |
SRA |
| |
|
| Source name |
Shew12222010.4
|
| Organism |
Shewanella sp. W3-18-1 |
| Characteristics |
condition: high light / high O2
strain: W3-18-1
|
| Treatment protocol |
The co-cultivation experiments were carried out in a modified A+ medium which was contained 17 mM NH4Cl and 10 µm FeCl3·6H2O. D,L-Na lactate or NaHCO3 were used as the sole source of carbon at 5 mM and 8 mM concentrations
|
| Growth protocol |
Shewanella W3-18-1 cultures were maintained at 30oC in tryptic soy broth or M1 defined medium amended with 20 mM D,L-Na lactate and 10 ml each of 10X Wolfe's vitamin and 10X mineral solutions (Kieft et al 1999). In chemostat cultures, Shewanella W3-18 was grown using 5 mM D,L-Na lactate as the sole source of C . Synechococcus 7002 was routinely grown in modified A+ media (Stevens and Porter 1980) at room temperature in 1-L Roux bottles sparged with 2% CO2-enriched air under continuous 50 µmolom-2os-1 illumination. Chemostat cultivation of Synechococcus 7002 was carried out using 8 mM NaHCO3 as the sole source of C in a white-light photobioreactor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol following by DNAseI treatment using Qiagen RNAseay mini column
Template cDNA was prepared using the Applied Biosystems SOLiD® Total RNA-Seq Kit (Life Technologies, Carlsbad, CA) according to manufacturer's protocol. Sequencing was carried using the SOLiDTM 5500XL protocol (Life Technologies).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Data processing |
The 50-base short read sequences produced by the 5500XL SOLiD sequencer were mapped in color space using SOLiD LifeScope software version 2.5 using the default parameters
Genome_build: Shewanella sp. W3-18-1: ASM1518v1; NC_008750
Genome_build: Synechococcus 7002: ASM1948v1; NC_010474, NC_010475, NC_010476, NC_010477, NC_010478, NC_010479 and NC_010480
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Dec 16, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Lye Meng Markillie |
| E-mail(s) |
Meng.markillie@pnnl.gov
|
| Phone |
509 371 7300
|
| Organization name |
Environmental Molecular Sciences Laboratory
|
| Department |
Biosystems Dynamics & Simulation
|
| Lab |
Cell Isolation and Systems Analysis
|
| Street address |
902 Battelle Blvd
|
| City |
Richland |
| State/province |
WA |
| ZIP/Postal code |
99352 |
| Country |
USA |
| |
|
| Platform ID |
GPL18075 |
| Series (1) |
| GSE53360 |
INTERACTIONS BETWEEN CYANOBACTERIA AND HETEROTROPHS UNDER DIFFERENT TROPHIC CONDITIONS |
|
| Relations |
| BioSample |
SAMN02444866 |
| SRA |
SRX392723 |
