GEO Dataset

GEO Dataset Dataset details
GDS ID 200030303
GDS Accession GSE30303
Title Reliable analysis of the catabolic gene landscape and transcriptome for pollutant degradation using a custom open source microarray with internal calibration
Summary Despite various efforts to develop tools to detect and compare the activity and catabolic potential and activity for pollutant degradation of microorganisms in environmental samples, an open-source, curated and reliable method is still required. Here we report on a customize normalization system that can be applied to any microarray design, allowing the assessment of reliability of signals and enabling cross-experiment comparisons. Probes for the underlying catabolic gene array were designed based on manually curated databases for catabolic key genes. Signals were assigned to the respective catabolic protein subfamily that allows to inferring the functions and substrate specificity. The placement of probes for critical degradation nodes and subsequent metabolic steps allows the retrieval of information on the metabolic net. Information on gene localization from genome surveys was correlated to signals of putative hosts to generate phylogenetic community information. Hence, this novel array system was validated using genomic DNA of genome sequenced bacterial strains hosting biodegradation functions and applied to genomic DNA and RNA extracted from environmental samples under aromatic pollution pressure.
Expression Profiles 0
Number of Samples 23
GEO Series GSE30303
GDS Data Type Expression profiling by array
Taxon unidentified microorganism; Ralstonia eutropha JMP134; Pseudomonas putida F1; Sphingomonas wittichii RW1; Burkholderia xenovorans LB400

Platforms

NameCatabolic microarray Version 2.1
Technology Typespotted oligonucleotide
AccessionGPL13771

GEO Samples

GEO Accession Condition
GSM751125 JMP134 1XSSC_55 degree C
GSM751115 Water 16 genomic DNA naphthalene
GSM751116 Water 14 RNA control
GSM751118 Water 16 RNA control
GSM751114 Water 16 genomic DNA control
GSM751130 LB400 2XSSC_55 degree C
GSM751128 LB400 0.1XSSC_55 degree C
GSM751112 Water 14 genomic DNA control
GSM751127 JMP134 3XSSC_50 degree C
GSM751124 JMP134 0.1XSSC_55 degree C
GSM751113 Water 14 genomic DNA naphthalene
GSM751122 F1 2XSSC_55 degree C
GSM751121 F1 1XSSC_55 degree C
GSM751129 LB400 1XSSC_55 degree C
GSM751117 Water 14 RNA naphthalene
GSM751120 F1 0.1XSSC_55 degree C
GSM751134 RW1 2XSSC_55 degree C
GSM751131 LB400 3XSSC_50 degree C
GSM751126 JMP134 2XSSC_55 degree C
GSM751119 Water 16 RNA naphthalene
GSM751132 RW1 0.1XSSC_55 degree C
GSM751123 F1 3XSSC_50 degree C
GSM751133 RW1 1XSSC_55 degree C