|
| Status |
Public on May 26, 2021 |
| Title |
MGHΔsoxSparB |
| Sample type |
SRA |
| |
|
| Source name |
30 min exposure paraquat 7.81µM MGH78578 ΔSoxS
|
| Organism |
Klebsiella pneumoniae |
| Characteristics |
strain: MGH 78578
genotype: {delta}SoxS
treatment: paraquat
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina HiSeq2500 RNA Sample Prep Kit was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Segemehl V0.18 used for mapping
Read counts were calculated custom made perl script.
Reads were normalized using VOOM transformation (Log2 normalized read counts) from Limma R package
Differential gene expression was calculated using Limma in R
Mapped reads were transformed into graphical "GR" files for visualisation uding IGB
Genome_build: Klebsiella pneumoniae MGH 78578
Supplementary_files_format_and_content: normalized values for each Sample.
|
| |
|
| Submission date |
Mar 11, 2020 |
| Last update date |
May 26, 2021 |
| Contact name |
Sathesh K Sivasankaran |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Missouri
|
| Lab |
Bioinformatics and Analytics Core
|
| Street address |
Bond Life Sciences Center Suite 106, 1201 Rollins Street
|
| City |
Columbia |
| State/province |
MO |
| ZIP/Postal code |
65211 |
| Country |
USA |
| |
|
| Platform ID |
GPL25164 |
| Series (1) |
| GSE146844 |
Analysis of the oxidative stress regulon identifies soxS as a genetic target for resistance reversal in multi-drug resistant Klebsiella pneumoniae |
|
| Relations |
| BioSample |
SAMN14360872 |
| SRA |
SRX7898257 |
