 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 29, 2015 |
| Title |
PAO1 WT replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
PAO1 WT replicate 2
|
| Organism |
Pseudomonas aeruginosa PAO1 |
| Characteristics |
genotype/variation: WT
strain: Laboratory strain
quorum sensing status: Quorum sensing intact
|
| Growth protocol |
Strains to be analyzed were grown overnight in LB, pelleted and washed, then resuspended to an OD600=1.0 in T-broth. 9, 5uL spots of this suspension were spotted onto T-broth agar and incubated at 1% O2, 5% CO2 for 12 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Colony biofilms of PAO1 and J215 wild type or Δanr were grown for 12 h, then harvested in 1 mL of PBS applied to the plate followed by recovery with an angled glass rod. Samples were pelleted by centrifugation and stored at -80°C. RNA was isolated from pelleted cells using the RNeasy mini kit (Qiagen), followed by treatment with RQ1 DNAase from Promega, both in accordance with manufacturers’ instructions. Ribosomal and transfer RNAs were removed using the MICROBExpress kit (Life Technologies) according to manufacturer's instructions.
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 |
Reads were trimmed for adaptor sequences and mapped to the PAO1 whole genome with CLC Genomics Workbench platform (v7.5.1) using default parameters.
Mapped reads were quantile normalized to all reads using CLC Genomics Workbench.
Fold change values and significance statistics between RNA Seq samples were calculated using the 'Empirical analysis of DGE' algorithm in CLC Genomics Workbench, which is a re-implementation of the "Exact Test" from the EdgeR Bioconductor package (Robinson and Smyth, Biostatistics, 2008)(Robinson et al., Bioinformatics, 2010), and was conducted between all pairs.
Genome_build: ASM676v1; PAO1 NC_002516
Supplementary_files_format_and_content: Processed data file is a data matrix that contains raw unique gene reads, quantile normalized reads, and calculated fold changes between WT and ∆anr samples.
|
| |
|
| Submission date |
May 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Deborah A Hogan |
| E-mail(s) |
[email protected]
|
| Organization name |
Geisel School of Medicine at Dartmouth
|
| Department |
Microbiology and Immunology
|
| Street address |
Vail Building Rm 208
|
| City |
Hanover |
| State/province |
NH |
| ZIP/Postal code |
03755 |
| Country |
USA |
| |
|
| Platform ID |
GPL18782 |
| Series (1) |
| GSE68534 |
Using RNA Seq to define the regulon of the Pseudomonas aeruginosa transcription factor Anr in low-oxygen colony biofilms. |
|
| Relations |
| BioSample |
SAMN03581444 |
| SRA |
SRX1017132 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
