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 | Burkholderia xenovorans LB400; unidentified microorganism; Ralstonia eutropha JMP134; Pseudomonas putida F1; Sphingomonas wittichii RW1 |
Platforms
Name | Catabolic microarray Version 2.1 |
Technology Type | spotted oligonucleotide |
Accession | GPL13771 |
GEO Samples
GEO Accession | Condition |
---|---|
GSM751121 | F1 1XSSC_55 degree C |
GSM751124 | JMP134 0.1XSSC_55 degree C |
GSM751112 | Water 14 genomic DNA control |
GSM751120 | F1 0.1XSSC_55 degree C |
GSM751132 | RW1 0.1XSSC_55 degree C |
GSM751130 | LB400 2XSSC_55 degree C |
GSM751113 | Water 14 genomic DNA naphthalene |
GSM751134 | RW1 2XSSC_55 degree C |
GSM751114 | Water 16 genomic DNA control |
GSM751116 | Water 14 RNA control |
GSM751115 | Water 16 genomic DNA naphthalene |
GSM751133 | RW1 1XSSC_55 degree C |
GSM751125 | JMP134 1XSSC_55 degree C |
GSM751119 | Water 16 RNA naphthalene |
GSM751123 | F1 3XSSC_50 degree C |
GSM751128 | LB400 0.1XSSC_55 degree C |
GSM751129 | LB400 1XSSC_55 degree C |
GSM751126 | JMP134 2XSSC_55 degree C |
GSM751122 | F1 2XSSC_55 degree C |
GSM751118 | Water 16 RNA control |
GSM751131 | LB400 3XSSC_50 degree C |
GSM751127 | JMP134 3XSSC_50 degree C |
GSM751117 | Water 14 RNA naphthalene |