 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 12, 2021 |
| Title |
cells from 115 h old biofilm rep 4 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial biofilm cells
|
| Organism |
Pseudomonas fragi |
| Characteristics |
strain: 1793
tissue: Bacterial biofilm cells
|
| Growth protocol |
P. fragi biofilms were grown on surface sterilized beef cuts kept at 10 P. fragi biofilms were grown on surface sterilized beef cuts kept at 10 ͦC under aerobic conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the RNeasy minikit (Qiagen, MD, cat no-74104) using the protocol for disruption of bacteria grown on solid media,
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 |
Galaxy platform was used for data analysis. Trimming of the reads were not due to high quality of data.
The reads were mapped to the P. fragi 1793 reference genome (Gene bank accession no NQKS00000000) with the Burrows-Wheeler Aligner (version 0.7.17) using the BWA-MEM algorithm. The mapped reads, which were in BAM format, were visualised using Jbrowse genome browser (version 1.16.4) to determine the efficiency of mapping. Mapped reads were used in subsequent analyses.
To estimate the number of genes overlapping with each gene in the reference genome, the SAM/BAM to count matrix of Galaxy was used.
Differential expression was examined using the Voom tool (Galaxy Version 0.28) ,
The gene expression of P. fragi in the three stages of the biofilm: (Initiation vs Maturation), (Initiation vs Dispersal), and (Maturation vs Dispersal) were compared pairwise using the DEGUST tool (http://degust.erc.monash.edu/).
Supplementary_files_format_and_content: Differential counts, xls format
|
| |
|
| Submission date |
Jan 11, 2021 |
| Last update date |
Jan 12, 2021 |
| Contact name |
Nirmani Wickramasinghe |
| E-mail(s) |
nirmani.wickramasinghe@postgrad.curtin.edu.au
|
| Phone |
0416695681
|
| Organization name |
CSIRO
|
| Department |
Public Health
|
| Street address |
671, Sneydes Road
|
| City |
Werribee |
| State/province |
VIC |
| ZIP/Postal code |
3030 |
| Country |
Australia |
| |
|
| Platform ID |
GPL29589 |
| Series (1) |
| GSE164539 |
RNA seq data of Pseudomonas fragi 1793 biofilms formed on aerobically stored, chilled beef |
|
| Relations |
| BioSample |
SAMN17282776 |
| SRA |
SRX9820261 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
