|
| Status |
Public on Oct 28, 2020 |
| Title |
XEN41_control_Exp5_t=48 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: Xen41 Tetracycline resistant
treatment: control
time: 48hr
|
| Treatment protocol |
solution was removed by centrifugation and bacteria+RNA stabilization solution (RNAlaterTM solution, invitrogen) were stored at -80°C prior to RNA extraction
|
| Growth protocol |
Hydroponic experiment in Growth Minimal medium (Rathnayake, I. V. N.; Megharaj, M.; Krishnamurti, G. S. R.; Bolan, N. S.; Naidu, R., Heavy metal toxicity to bacteria – Are the existing growth media accurate enough to determine heavy metal toxicity? Chemosphere. 2013, 90, (3), 1195-1200.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNeasy® Mini Kit QIAGEN
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
53-Sample-David-O-RNAseq_S53
|
| Data processing |
Data processing (trimming using AdapterRemoval, Alignment using BWA, quantification using featureCounts/R)
Quality control assessment using FastQC
Data filtering for low counts and transcriptional profiling (Table of expression levels for all samples)
Differential gene expression across groups using edgeR and limma
Basic Gene Ontology Enrichment Analysis based on data from the [Pseudomonas Genome Database](https://www.pseudomonas.com/)
Genome_build: GCF_000006765.1 ASM676v1 genomic
Supplementary_files_format_and_content: countTable.tsv
|
| |
|
| Submission date |
Oct 27, 2020 |
| Last update date |
Oct 28, 2020 |
| Contact name |
James Breen |
| E-mail(s) |
jimmy.breen@telethonkids.org.au
|
| Organization name |
Australian National University
|
| Department |
John Curtin School of Medical Research
|
| Lab |
Black Ochre Data Labs (Adelaide)
|
| Street address |
108 North Terrace (Ground Floor)
|
| City |
Adelaide |
| State/province |
SA |
| ZIP/Postal code |
5000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL21297 |
| Series (2) |
| GSE160187 |
Do Copper enhance antibiotic resistance (AR) in resistant bacteria and/or induce AR in sensitive bacteria? [RNA-seq] |
| GSE160190 |
Do Copper enhance antibiotic resistance (AR) in resistant bacteria and/or induce AR in sensitive bacteria? |
|
| Relations |
| BioSample |
SAMN16562276 |
| SRA |
SRX9370137 |
