|
| Status |
Public on Apr 04, 2022 |
| Title |
L_D_T2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial Transcriptome
|
| Organism |
Methylorubrum extorquens AM1 |
| Characteristics |
strain: M. extorquens AM1 + pCM160
sampling point: T2
cultivation time [h]: 22.75
replicate: Control strain replicate 3
purpose: Control
|
| Treatment protocol |
Cultures were treated equally, half of the strains contained a production plasmid (pCM160_RBS_YciAHI = "P"), half of the strains contained a empty plasmid control (pCM160 = "L")
|
| Growth protocol |
M. extorquens AM1 main cultures were inoculated from 48 h old preculture and grown in methanol minimal medium with 50µg/mL kanamycin in shake flasks at 30°C. For stabilization of RNA, one volume of growing bacterial culture (> 10^6 cells) was mixed with two volumes of RNAprotect Bacteria Reagent from QIAGEN and incubated for 5 minutes. Cells were centrifuged for 10 min at 5000 g to remove supernatant and stored pelleted at 80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The GenXPro standard treatment for isolation of RNA from bacteria was used (isolation and DNAse treatment, depletion of rRNA, library preparation)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The GenXPro standard data processing pipeline was used.
Data was normalized with CPM Method
Reads were annotated according to NCBI reference genome
Assembly: NC_012807, NC_012808, NC_012809, NC_012810, NC_012811
Supplementary files format and content: matrix table of raw counts (all features)
Supplementary files format and content: matrix table of counts (all features), CPM-normalized and annotated
|
| |
|
| Submission date |
Apr 01, 2022 |
| Last update date |
Apr 07, 2022 |
| Contact name |
Laura Pöschel |
| Organization name |
Dechema Forschungsinstitut
|
| Department |
Microbial Biotechnology
|
| Lab |
Markus Buchhaupt
|
| Street address |
Theodor-Heuss-Allee 25
|
| City |
Frankfurt |
| State/province |
Hessen |
| ZIP/Postal code |
60486 |
| Country |
Germany |
| |
|
| Platform ID |
GPL32105 |
| Series (1) |
| GSE199961 |
Improvement of dicarboxylic acid production with Methylorubrum extorquens by reduction of product reuptake |
|
| Relations |
| BioSample |
SAMN27177978 |
| SRA |
SRX14712804 |
