 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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 |
| E-mail(s) |
Pierre.PEYRET@univ-bpclermont.fr
|
| Phone |
+33473405139
|
| 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 |
| |
|
| 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) |
| GSM707932 |
gDNA from contaminated site B, campaign 2, well P1 (SBC2P1) |
| GSM707933 |
gDNA from contaminated site B, campaign 2, well P2 (SBC2P2) |
| GSM707934 |
gDNA from contaminated site B, campaign 2, well P3 (SBC2P3) |
| GSM707935 |
gDNA from contaminated site B, campaign 2, well P4 (SBC2P4) |
| GSM707936 |
gDNA from contaminated site B, campaign 3, well P1 (SBC3P1) |
| GSM707937 |
gDNA from contaminated site B, campaign 3, well P2 (SBC3P2) |
| GSM707938 |
gDNA from contaminated site B, campaign 3, well P3 (SBC3P3) |
| GSM707939 |
gDNA from contaminated site B, campaign 3, well P4 (SBC3P4) |
| GSM707940 |
gDNA from contaminated site B, campaign 4, well P1 (SBC4P1) |
| GSM707941 |
gDNA from contaminated site B, campaign 4, well P2 (SBC4P2) |
| GSM707942 |
gDNA from contaminated site B, campaign 4, well P3 (SBC4P3) |
| GSM707943 |
gDNA from contaminated site B, campaign 4, well P4 (SBC4P4) |
| GSM707944 |
gDNA from contaminated site B, campaign 5, well P1 (SBC5P1) |
| GSM707945 |
gDNA from contaminated site B, campaign 5, well P2 (SBC5P2) |
| GSM707946 |
gDNA from contaminated site B, campaign 5, well P3 (SBC5P3) |
| GSM707947 |
gDNA from contaminated site B, campaign 5, well P4 (SBC5P4) |
| GSM707948 |
gDNA from contaminated site F, well P1 (SFP1) |
| GSM707949 |
gDNA from contaminated site F, well P2 (SFP2) |
| GSM707950 |
gDNA from contaminated site F, well P3 (SFP3) |
| GSM707951 |
gDNA from contaminated site F, well P4 (SFP4) |
| GSM707952 |
gDNA from contaminated site G, well P1 (SGP1) |
| GSM707953 |
gDNA from contaminated site G, well P3 (SGP3) |
| GSM707954 |
gDNA from contaminated site G, well P4 (SGP4) |
| GSM707955 |
gDNA from contaminated site H, well P1 (SHP1) |
| GSM707956 |
gDNA from contaminated site H, well P2 (SHP2) |
| GSM707957 |
gDNA from contaminated site H, well P3 (SHP3) |
| GSM707958 |
gDNA from contaminated site H, well P4 (SHP4) |
|
| This SubSeries is part of SuperSeries: |
| GSE28609 |
Monitoring of functional gene responses to biostimulation from TCE-contaminated sites using a functional microarray |
|
| Relations |
| BioProject |
PRJNA143085 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE28606_RAW.tar |
61.2 Mb |
(http)(custom) |
TAR (of PAIR) |
| Processed data included within Sample table |
|
|
|
|
 |
Less...
More...