|
| Status |
Public on Sep 01, 2021 |
| Title |
uni-0956B: VCA0956, uninduced, replicate B |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria RNA
|
| Organism |
Shigella flexneri 2a str. 2457T |
| Characteristics |
condition: -IPTG
growth: LB + DOC, mid-log
|
| Treatment protocol |
Induction of the pTac promoter of VCA0956 using IPTG (100 μM)
|
| Growth protocol |
S. flexneri grown in LB + DOC (0.05% w/v), supplemented with Kanamycin (50 μg/ml) to maintain pVCA0956. Cultures incubated at 37 C, shaking at 220 rpm for 3 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Purelink RNA Mini Kit (Thermo Fisher, 12183020) using the manufacturers protocol with Trizol reagent
RNA libraries were prepared for sequencing using standard protocols (Genewiz). Sequencing was performed by Genewiz.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Set paired end reads (Geneious)
Raw sequences were trimmed using BBDuk (Geneious)
Reads were mapped to reference (AE014073.1, AF386526.1, AF250878, and VCA0956 from NC_002506) using Geneious mapper
Expression analysis was carried out to determine RPKM, FPKM and TPM (Geneious)
Supplementary_files_format_and_content: .xlsx file contains mapping and differential expression for each Shigella gene
|
| |
|
| Submission date |
May 03, 2021 |
| Last update date |
Sep 01, 2021 |
| Contact name |
Ben James Koestler |
| Organization name |
Western Michigan University
|
| Department |
Biological Sciences
|
| Lab |
Koestler
|
| Street address |
1903 West Michigan Avenue, 3119 Wood Hall
|
| City |
Kalamazoo |
| State/province |
MI |
| ZIP/Postal code |
49008 |
| Country |
USA |
| |
|
| Platform ID |
GPL30069 |
| Series (1) |
| GSE173759 |
Cyclic di-GMP Regulates Shigella flexneri Pathogenesis |
|
| Relations |
| BioSample |
SAMN18986023 |
| SRA |
SRX10759805 |
