|
| Status |
Public on Feb 13, 2018 |
| Title |
T1G2 |
| Sample type |
SRA |
| |
|
| Source name |
Gammaproteobacteria isolated from El Yunque forest, Puerto Rico
|
| Organism |
[Enterobacter] lignolyticus SCF1 |
| Characteristics |
treatment: 60 mM Glucose
phase: Mid-exponential phase
biological replicates: Rep2
|
| Treatment protocol |
Two conditions: 1) unamended control cultures: using glucose (60 mM) as main carbon source 2) lignin-amended treatment: using glucose (60 mM) as main carbon source + lignin (0.1%)
|
| Growth protocol |
Cells were grown in anaerobic modified LS4D minimal media
|
| 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.
|
| |
|
| 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
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Mar 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Lye Meng Markillie |
| E-mail(s) |
[email protected]
|
| 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 |
GPL23197 |
| Series (1) |
| GSE96828 |
Multi-time series RNA-Seq analysis of Enterobacter lignolyticus SCF1during growth in lignin-amended medium |
|
| Relations |
| BioSample |
SAMN06622150 |
| SRA |
SRX2658011 |
