|
| Status |
Public on Sep 13, 2017 |
| Title |
HL-48 Xylose Rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Halomonas sp. HL-48
|
| Organism |
Halomonas sp. HL48 |
| Characteristics |
carbon source: Growth on xylose
growth condition: Axenic
|
| Treatment protocol |
Strains were grown either axenically or in co-culture with glucose, in co-culture with xylose or axenically with xylose (Halomonas sp. HL-48 only).
|
| Growth protocol |
These strains were grown under both axenic and co-culture conditions in a defined media named Hot Lake Heterotrophic (HLH) medium: 400 mM MgSO4·7H2O, 80 mM Na2SO4, 20 mM KCl, 0.189 mM Na2CO3, 0.175 mM K2HPO4, 5 mM NH4Cl, 10 mM TES, 22.3 µM NH4Fe(III) citrate, 10 mM NaHCO3. HLH was amended with 1× Wolfe's vitamins 21 and with either glucose or xylose (to 5 mM) as the sole carbon source
|
| 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 |
| |
|
| Description |
HL48_Norm_Exp_Values.csv
T19
|
| 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
Counts were then determined for each gene in either Halomonas sp. HL-48 and Marinobacter sp. HL-58 using SOLiD LifeScope software version 2.5 using the default parameters
Normalized expression values and differentially expressed genes were then determined using DESeq2
Genome_build: Nucleotide sequence is available through the European Nucleotide Archive (http://www.ebi.ac.uk/ena) under accessions GCA_000686925.1 (Halomonas sp. HL-48) and GCA_000686085.1 (Marinobacter sp. HL-58), and annotated genome data is available through IMG (http://img.jgi.doe.gov).
Supplementary_files_format_and_content: HL48_Norm_Exp_Values.csv (Normalized expression values for HL-48), HL58_Norm_Exp_Values.csv (Normalized expression values for HL-58)
|
| |
|
| Submission date |
Sep 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ryan Scott McClure |
| E-mail(s) |
[email protected]
|
| Organization name |
Pacific Northwest National Laboratory
|
| Street address |
902 Battelle Boulevard
|
| City |
Richland |
| State/province |
Washington |
| ZIP/Postal code |
99354 |
| Country |
USA |
| |
|
| Platform ID |
GPL24006 |
| Series (1) |
| GSE103773 |
Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture |
|
| Relations |
| BioSample |
SAMN07637233 |
| SRA |
SRX3181549 |
