|
| Status |
Public on Jun 12, 2014 |
| Title |
PAOMS.1_2 |
| Sample type |
SRA |
| |
|
| Source name |
planktonic culture
|
| Organism |
Pseudomonas aeruginosa PAO1 |
| Characteristics |
strain: PAO1_∆mutS
agent: none
|
| Treatment protocol |
Cells from 3 pooled cultures were harvested by addition of the same volume of RNA-protect buffer (Qiagen) and centrifugation.
|
| Growth protocol |
Cultures growing in LB medium at 37 °C were harvested after reaching an OD600 of 1.0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Using Rneasy kit (Qiagen) plus Qiashredder columns.
Customized protocol (Dötsch et al., PloS ONE, 2012). Bacterial rRNA was depleted using MICROBExpress kit with the Pseudomonas module (Ambion) and fragmented by sonication using Covaris Adaptive Acoustics device (Covaris). Upon ligation of barcoded adapters, reverse transcription with SuperScript II kit (Invitrogen) followed. Amplification was done by PCR using Illumina platform compatible primers. Established cDNA library was normalized by double strand specific nuclease treatment (Evrogen) according DSN Normalization Sample Preparation Guide from Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
PAO1_∆mutS_derived_mutant1_duplicate2
|
| Data processing |
RNA-seq reads were trimmed and mapped to the PAO1 genome using the Stampy aligner with default settings.
The Reads-per-Gene were calculated from the SAM files counting only the reads that were located within the gene boundaries
Mutations were identified using samtools version 0.1.18
Genome_build: ASM676v1
Supplementary_files_format_and_content: The processed files in TXT format include either Genes and Reads-per-gene (.rpg) or lists of called mutations (.flt.vcf)
|
| |
|
| Submission date |
Jun 11, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Denitsa Eckweiler |
| E-mail(s) |
[email protected]
|
| Organization name |
Technische Universität Braunschweig
|
| Department |
Institute of Microbiology
|
| Lab |
Prof. Dieter Jahn
|
| Street address |
Spielmannstr. 7
|
| City |
Braunschweig |
| State/province |
Lower Saxony |
| ZIP/Postal code |
D-38106 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18782 |
| Series (1) |
| GSE58390 |
Pseudomonas aeruginosa Ceftolozane-Tazobactam Resistance Development Requires Multiple Mutations Leading to Overexpression and Structural Modification of AmpC. |
|
| Relations |
| BioSample |
SAMN02851341 |
| SRA |
SRX591677 |
