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| Status |
Public on Apr 03, 2012 |
| Title |
Monitoring of functional gene responses to biostimulation from a TCE-contaminated site |
| Platform organisms |
Shewanella; Pseudomonas; Methylosinus; Nitrosomonas; Mycobacterium; Geobacter; Thauera; Desulfitobacterium; Dehalobacter; Sulfurospirillum; Dehalococcoides |
| Sample organism |
groundwater metagenome |
| Experiment type |
Expression profiling by array
|
| Summary |
A functional microarray targeting 24 genes involved in chlorinated solvent biodegradation pathways has been developed and used to monitor the gene expression in a contaminated site (site B) under ERD (enhanced reductive dechlorination) treatment. The microarray format provided by NimbleGen and used in this study is 12x135K. 4 µg of labelled antisense mRNA from 3 groundwater samples were hybridized on the microarray.
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| Overall design |
A 3-chip study was performed, each corresponding to hybridization with 4 µg of labelled antisense mRNA retrieved from a monitoring well of a contaminated site (site B). Each probe (760nt) on the microarray was synthesized in eight replicates, and a total of 5,707 random probes was used to determine the background noise.
Groundwater samples were collected from a contaminated site (site B) from three monitoring wells (P1, P2 and P3). P1: well located upstream to the contamination source. P2: well in the contamination source. P3 : well located downstream to the contamination source.
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| Contributor(s) |
Dugat-Bony E, Biderre-Petit C, Jaziri F, Denonfoux J, Boucher D, Peyretaillade E, Peyret P |
| Citation(s) |
22432919 |
| |
| Submission date |
Apr 13, 2011 |
| Last update date |
Apr 05, 2012 |
| Contact name |
Peyret Pierre |
| E-mail(s) |
[email protected]
|
| Phone |
+33473405139
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| Organization name |
CNRS - Blaise Pascal University
|
| Lab |
Laboratory Microorganisms: Genome and Environment
|
| Street address |
24, avenue des landais
|
| City |
AUBIERE |
| ZIP/Postal code |
63177 |
| Country |
France |
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| Platforms (1) |
| GPL13409 |
NimbleGen_Custom_Chloroethene_array_V02 |
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| Samples (3) |
| GSM707969 |
antisense mRNA from contaminated site B, campaign 5, well P1 (SBC5P1) |
| GSM707970 |
antisense mRNA from contaminated site B, campaign 5, well P2 (SBC5P2) |
| GSM707971 |
antisense mRNA from contaminated site B, campaign 5, well P3 (SBC5P3) |
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| This SubSeries is part of SuperSeries: |
| GSE28609 |
Monitoring of functional gene responses to biostimulation from TCE-contaminated sites using a functional microarray |
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| Relations |
| BioProject |
PRJNA143087 |
