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Series GSE28606 Query DataSets for GSE28606
Status Public on Apr 03, 2012
Title Monitoring of functional gene responses to ERD (enhanced reductive dechlorination) from four TCE-contaminated sites
Platform organisms Shewanella; Pseudomonas; Methylosinus; Nitrosomonas; Mycobacterium; Geobacter; Thauera; Desulfitobacterium; Dehalobacter; Sulfurospirillum; Dehalococcoides
Sample organism groundwater metagenome
Experiment type Genome variation 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 diversity present in four trichloroethylene (TCE) contaminated sites under ERD (enhanced reductive dechlorination) treatment. The microarray format provided by NimbleGen and used in this study is 12x135K. 2 µg of labelled gDNA from 30 groundwater samples were hybridized on the microarrays.
Overall design A 30-chip study was performed, each chip corresponding to hybridization with 2 µg of labelled gDNA retrieved from a monitoring well from one of the four contaminated sites. 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 four contaminated sites (B, F, G and H), four monitoring wells per site (P1, P2, P3 and P4). P1: well located upstream to the contamination source. P2: well in the contamination source. P3 and P4: wells located downstream to the contamination source. For site B, the monitoring of ERD demonstration was performed through a total of 5 sampling campaigns: C1 (T=0), C2 (T=104 days), C3 (T=231 days), C4 (T=291 days) and C5 (T=378 days). For the three other sites (F, G and H), only one sampling campaign was performed after the treatment.
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
Phone +33473405139
Organization name CNRS - Blaise Pascal University
Lab Laboratory Microorganisms: Genome and Environment
Street address 24, avenue des landais
ZIP/Postal code 63177
Country France
Platforms (1)
GPL13409 NimbleGen_Custom_Chloroethene_array_V02
Samples (30)
GSM707929 gDNA from contaminated site B, campaign 1, well P1 (SBC1P1)
GSM707930 gDNA from contaminated site B, campaign 1, well P2 (SBC1P2)
GSM707931 gDNA from contaminated site B, campaign 1, well P4 (SBC1P4)
This SubSeries is part of SuperSeries:
GSE28609 Monitoring of functional gene responses to biostimulation from TCE-contaminated sites using a functional microarray
BioProject PRJNA143085

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE28606_RAW.tar 61.2 Mb (http)(custom) TAR (of PAIR)
Processed data included within Sample table

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