Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 2
Release date: Aug 25 2009
Last update date: Oct 20 2017
Access: Public
Chemicals: PQQ Cofactor
Dataset link Microarray studies of pqqE disruption mutant vs wild type

Experimental Protocol


All the genes subjected to microarray analysis are as described in the genome sequence of bacterium available at ftp://ftp.ncbi.nih.gov/genomes/bacteria/Deinococcus_radiodurans. Oligonucleotides designed to represent the respective predicted ORFs of Deinococcus radiodurans ((NC_001263, NC_001264, NC_000958, NC_000959) are synthesized and purified by hydrophobic column on HPLC. The oligonucleotides are deposited on to poly-L-Lysine slide in triplicate. Microarrays were scanned using Gene Pix 4000B and hybridization signals were quantified using GenePix Pro 5.1. Prior to channel normalization, microarray outputs were filtered to remove spots of poor signal quality by excluding those data points with a mean intensity by less that 2 standard deviation above background in both channels. Normalization of data and its statistical analysis were carried out in the R computing environment using linear models for microarray data package (Limma). Using this tool, the global LOESS normalization was carried out for each microarray. The 3- replicate spots per gene in each array were used to maximize the robustness of differential expression measurements of each gene via the “lmFit” function within Limma. Two biological replicates were carried out for transcriptome analysis of pqqE mutant strain against wild type cells.

Repositories


GEO

GSE17724

ArrayExpress

E-GEOD-17724

BioProject

PRJNA118441

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Contact


Hari Misra
Hari S Misra