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| Status |
Public on Jun 01, 2009 |
| Title |
Expression of lignin-degrading enzymes in soils using targeted microarrays |
| Platform organisms |
Cryphonectria parasitica; Neurospora crassa; Phlebia radiata; Pleurotus ostreatus; Pleurotus eryngii; Trametes versicolor; Schizophyllum commune; Agaricus bisporus; Lentinula edodes; Fusarium oxysporum; Trametes cinnabarina; Heterobasidion annosum; synthetic construct; Botrytis cinerea; Gelatoporia subvermispora; Coriolopsis gallica; Dichomitus squalens; Trametes coccinea; Fusarium proliferatum; Phanerodontia chrysosporium |
| Sample organisms |
synthetic construct; unidentified; Phanerodontia chrysosporium |
| Experiment type |
Expression profiling by array
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| Summary |
Microarrays have become established tools for describing microbial systems, however the assessment of expression profiles for environmental microbial communities still presents unique challenges. Notably, the concentration of particular transcripts are likely very dilute relative to the pool of total RNA, and PCR-based amplification strategies are vulnerable to amplification biases and the appropriate primer selection. Thus, we apply a signal amplification approach, rather than template amplification, to analyze the expression of selected lignin-degrading enzymes in soil. Controls in the form of known amplicons and cDNA from Phanerochaete chrysosporium were included and mixed with the soil cDNA both before and after the signal amplification in order to assess the dynamic range of the microarray. We demonstrate that restored prairie soil expresses a diverse range of lignin-degrading enzymes following incubation with lignin substrate, while farmed agricultural soil does not. The mixed additions of control cDNA with soil cDNA indicate that the mixed biomass in the soil does interfere with low abundance transcript changes, nevertheless our microarray approach consistently reports the most robust signals.
Keywords: comparative analysis, microbial ecology, soil microbial communities
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| Overall design |
We used lignin degradation as a model process to demonstrate the use of an oligonucleotide microarray for directly detecting gene expression in soil communities using signal amplification instead of template amplification to avoid the introduction of PCR bias. In the current study, we analyzed mRNA isolated from two distinct soil microbial communities and demonstrate our ability to detect the expression of a small subset of lignin degrading genes following exposure to a lignitic substrate. We also included purified control amplicons and mixed target experiments with pure P. chrysosporium genomic cDNA to determine the level of interference from soil biomass on target hybridization.
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| Contributor(s) |
Bailey VL, Fansler SJ, Waters KM |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Dec 15, 2008 |
| Last update date |
Mar 20, 2012 |
| Contact name |
Katrina M Waters |
| E-mail(s) |
katrina.waters@pnl.gov
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| Organization name |
Pacific Northwest National Laboratory
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| Department |
Biological Sciences Division
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| Street address |
902 Battelle Blvd; MSIN J4-18
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| City |
Richland |
| State/province |
WA |
| ZIP/Postal code |
99352 |
| Country |
USA |
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| Platforms (1) |
| GPL7797 |
PNL mixed species lignin-degrading enzymes microarray |
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| Samples (68)
|
| GSM351212 |
buffer only, rep4 |
| GSM351213 |
buffer only, rep5 |
| GSM351214 |
buffer only, rep6 |
| GSM351215 |
treatment 1, rep1 |
| GSM351216 |
treatment 1, rep2 |
| GSM351217 |
treatment 1, rep3 |
| GSM351218 |
treatment 1, rep4 |
| GSM351219 |
treatment 1, rep5 |
| GSM351220 |
treatment 1, rep6 |
| GSM351221 |
treatment 1, rep7 |
| GSM351222 |
treatment 2, rep1 |
| GSM351223 |
treatment 2, rep2 |
| GSM351224 |
treatment 2, rep3 |
| GSM351225 |
treatment 2, rep4 |
| GSM351226 |
treatment 2, rep5 |
| GSM351227 |
treatment 2, rep6 |
| GSM351228 |
treatment 2, rep7 |
| GSM351229 |
treatment 2, rep8 |
| GSM351230 |
treatment 3, rep1 |
| GSM351231 |
treatment 3, rep2 |
| GSM351232 |
treatment 3, rep3 |
| GSM351233 |
treatment 3, rep4 |
| GSM351234 |
treatment 3, rep5 |
| GSM351235 |
treatment 3, rep6 |
| GSM351236 |
treatment 3, rep7 |
| GSM351237 |
treatment 3, rep8 |
| GSM351238 |
treatment 4, rep1 |
| GSM351239 |
treatment 4, rep2 |
| GSM351240 |
treatment 4, rep3 |
| GSM351241 |
treatment 4, rep4 |
| GSM351242 |
treatment 4, rep5 |
| GSM351243 |
treatment 4, rep6 |
| GSM351244 |
treatment 4, rep7 |
| GSM351245 |
treatment 4, rep8 |
| GSM351246 |
treatment 5, rep1 |
| GSM351247 |
treatment 5, rep2 |
| GSM351248 |
treatment 5, rep3 |
| GSM351249 |
treatment 5, rep4 |
| GSM351250 |
treatment 5, rep5 |
| GSM351251 |
treatment 5, rep6 |
| GSM351252 |
treatment 5, rep7 |
| GSM351253 |
treatment 5, rep8 |
| GSM351254 |
treatment 5, rep9 |
| GSM351255 |
treatment 5, rep10 |
| GSM351256 |
treatment 5, rep11 |
| GSM351257 |
treatment 5, rep12 |
| GSM351258 |
treatment 6, rep1 |
| GSM351259 |
treatment 6, rep2 |
| GSM351260 |
treatment 6, rep3 |
| GSM351261 |
treatment 6, rep4 |
| GSM351262 |
treatment 6, rep5 |
| GSM351263 |
treatment 6, rep6 |
| GSM351264 |
treatment 6, rep7 |
| GSM351265 |
treatment 7, rep1 |
| GSM351266 |
treatment 7, rep2 |
| GSM351267 |
treatment 7, rep3 |
| GSM351268 |
treatment 7, rep4 |
| GSM351269 |
treatment 7, rep5 |
| GSM351270 |
treatment 7, rep6 |
| GSM351271 |
treatment 7, rep7 |
| GSM351272 |
treatment 7, rep8 |
| GSM351273 |
treatment 8, rep1 |
| GSM351274 |
treatment 8, rep2 |
| GSM351275 |
treatment 8, rep3 |
| GSM351276 |
treatment 8, rep4 |
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| Relations |
| BioProject |
PRJNA110233 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE13977_RAW.tar |
690.0 Kb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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