|
| Status |
Public on Nov 07, 2022 |
| Title |
RNA_KP13 |
| Sample type |
SRA |
| |
|
| Source name |
Pus Aspirate
|
| Organism |
Klebsiella pneumoniae |
| Characteristics |
cell type: bacterial cells
|
| Treatment protocol |
The plates were impregnated with colistin and/ or carbapenems to inhibit all but carbapenem and/or colistin-resistant isolates
|
| Growth protocol |
isolates on the swabs were grown in an enrichment broth overnight prior to plating on a blood plate
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Zymo DNA extraction kits were used to extract DNA for PCR confirmation of the resistance genes
HMW gDNA was isolated using NEB Mornach HMW DNA isolation kit (https://international.neb.com/protocols/2020/10/27/protocol-for-high-molecular-weight-dna-hmw-dna-extraction-from-bacteria). HMW gDNA was quantified using Qubit HS dsDNA Assay and qualified on Tapestation using genomics screentape. HMW gDNA was shared to ~10kb fragments using covaries g-Tubes and QC’d using the above method. SMRTbell libraries were performed using PacBio’s Microbial Multiplexing workflow (see attached) The resulting libraries were size selected using BluePippin Size selection using U1 marker (10-18kb). QC was performed using the above method. Libraries were then prepared for sequencing following the online SMRTlink guided protocol (Binding kit 2.0 and Control 1.0, Sequel II Sequencing plate 2.0 and SMRT cell 8M.)
size selection was done by Blue-Pippin and sequenced with PacBio for DNA WGS
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Processed data for this sample are included in files included on other samples.
|
| Data processing |
All analysis was conducted within SMRTLINK v10.1
|
| |
|
| Submission date |
Nov 02, 2022 |
| Last update date |
Nov 07, 2022 |
| Contact name |
John Osei Sekyere |
| E-mail(s) |
[email protected]
|
| Phone |
0123192251
|
| Organization name |
University of Pretoria
|
| Department |
Department of Medical Microbiology
|
| Lab |
Molecular Microbiology
|
| Street address |
05 Bopheloweg Off Dr. Savage Road
|
| City |
Pretoria |
| State/province |
Gauteng |
| ZIP/Postal code |
0084 |
| Country |
South Africa |
| |
|
| Platform ID |
GPL32755 |
| Series (1) |
| GSE217148 |
Genomic and Transcriptional Characterisation of Carbapenem and Colistin Resistance Mechanisms in Klebsiella pneumoniae |
|
| Relations |
| BioSample |
SAMN29928034 |
| SRA |
SRX18138696 |
