|
| Status |
Public on Aug 01, 2018 |
| Title |
RNA sequencing of Mycobacterium dioxanotrophicus PH-06 treated with glucose |
| Sample type |
SRA |
| |
|
| Source name |
PH-06 cells grown on glucose
|
| Organism |
Mycobacterium dioxanotrophicus |
| Characteristics |
phenotype: Dioxane degrader
strain: PH-06
|
| Treatment protocol |
PH-06 cells in exponential phase (when half of the added substrates were consumed) were centrifuged and washed with AMS medium three times before total RNA extraction.
|
| Growth protocol |
Mycobacterium dioxanotrophicus PH-06 was grown in ammonium mineral salts (AMS) medium amended with 500 mg/L of dioxane as the carbon source.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA extraction was performed according to the protocol of RNase Mini Kit (Qiagen, Hilden, Germany).
mRNA libraries were prepared following Illumina mRNA-Seq Sample Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Extracted from PH-06 cells after grown on glucose
|
| Data processing |
Raw reads were mapped to the whole genome sequencing of PH-06
The relative gene expression levels were estimated using EDGE-pro v 1.3.1 (http://ccb.jhu.edu/software/EDGE-pro/)
Genome_build: CP020809-CP020813
Supplementary_files_format_and_content: Excel file; gene expression fold and raw read count
|
| |
|
| Submission date |
Aug 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ya He |
| E-mail(s) |
yh38@rice.edu
|
| Phone |
8329752665
|
| Organization name |
Rice University
|
| Department |
Department of Civil and Environmental Engineering
|
| Street address |
6100 MAIN ST, MS-519
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77005 |
| Country |
USA |
| |
|
| Platform ID |
GPL23948 |
| Series (1) |
| GSE103019 |
RNA Sequencing of Mycobacterium dioxanotrophicus PH-06 |
|
| Relations |
| BioSample |
SAMN07550178 |
| SRA |
SRX3122162 |
