|
| Status |
Public on Feb 08, 2023 |
| Title |
Bp wildtype rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
gram negative bacterium
|
| Organism |
Burkholderia pseudomallei |
| Characteristics |
cell type: gram negative bacterium
genotype: WT
treatment: overnight growth, and subculture to expoenential phase
|
| Growth protocol |
Bp wildtype strain1026b and sapR::T24 insertion mutant, were grown overnight in 3 ml LB broth in a 37 oC shaking incubator, subcultured to grow to mid exponential phase for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from 12 ml culture of each strain was isolated using TRIzol® reagent and purify through QIAGEN RNeasy plus mini kit according to the manufacturer’s instructions.
Sequencing was performed by the Tufts University Core Facility Genomics on the Illumina HiSeq 2500 platform after rRNA depletion and library generation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ChrI_II1046vsWT.xlsx
|
| Data processing |
Rockhopper tool designed specifically for analysis of bacterial RNA-Seq was used for the analysis
Supplementary files format and content: .xlsx files include RPKM and normalized expression from triplicates of each strain
|
| |
|
| Submission date |
Dec 08, 2022 |
| Last update date |
Feb 08, 2023 |
| Contact name |
Tung Hoang |
| E-mail(s) |
tongh@hawaii.edu
|
| Organization name |
University of Hawaii at Manoa
|
| Department |
School of life sciences
|
| Lab |
LSB318
|
| Street address |
1800 East-west Road
|
| City |
Honolulu |
| State/province |
Hi |
| ZIP/Postal code |
96822 |
| Country |
USA |
| |
|
| Platform ID |
GPL32930 |
| Series (1) |
| GSE220579 |
Transcriptome profiling of Burkholderia pseudomallei wildtype strain1026b and BP1026b_II1046::T4 insertion mutant |
|
| Relations |
| BioSample |
SAMN32118065 |
| SRA |
SRX18543710 |
