|
| Status |
Public on Dec 21, 2022 |
| Title |
CN32_fliAn_2 |
| Sample type |
SRA |
| |
|
| Source name |
CN-32 fliAn mutant
|
| Organism |
Shewanella putrefaciens |
| Characteristics |
genotype: CN-32 fliAn mutant
geographical location: Germany: Giessen
|
| Treatment protocol |
directly after cultivation the cells were treated with one volume of RNAprotect (Qiagen), incubated for 10 minutes at room temperature, centrifuged at 10.000 rpm and cell pellets were frozen at -80°C
|
| Growth protocol |
cell were grown in LB to an OD600 =0.d at 30C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNeasy Mini Kit (Qiagen) in combination with Qiashredder columns (Qiagen) was used according to the manufacturer’s instruction
The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
geographical location: Germany: Gießen
Cells were grown in LB to an OD600 =0.5 at 30C and incubated for 10 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.
|
| Data processing |
mRNA reads were trimmed using the tool ‘cutadapt’ (version 3.5) with default settings and mapped to the NC_009438.1 (Shewanella putrefaciens CN-32) reference genome from NCBI using ‘bowtie2’ (version 2.3.5.1) with default settings for single-end sequencing.
Assembly: NC_009438.1 (Shewanella putrefaciens CN-32)
Supplementary files format and content: raw unique gene reads.
|
| |
|
| Submission date |
Jul 05, 2022 |
| Last update date |
Dec 21, 2022 |
| Contact name |
Susanne Häußler |
| E-mail(s) |
[email protected]
|
| Organization name |
Twincore
|
| Department |
Molecular Bacteriology
|
| Street address |
Feodor-Lynen-Str. 7
|
| City |
Hanover |
| ZIP/Postal code |
30625 |
| Country |
Germany |
| |
|
| Platform ID |
GPL32422 |
| Series (1) |
| GSE207531 |
Constant production of FlhG ensures proper function of the flagellar counter in Shewanella putrefaciens |
|
| Relations |
| BioSample |
SAMN29535123 |
| SRA |
SRX16035512 |
