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Sample GSM1674728 Query DataSets for GSM1674728
Status Public on Jun 29, 2015
Title PAO1 ∆anr replicate 2
Sample type SRA
 
Source name PAO1 ∆anr replicate 2
Organism Pseudomonas aeruginosa PAO1
Characteristics genotype/variation: {delta}anr
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 SAMN03581446
SRA SRX1017134

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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