|
| Status |
Public on Jan 01, 2011 |
| Title |
UT2_top |
| Sample type |
genomic |
| |
|
| Source name |
Axel Heiberg Island
|
| Organism |
environmental samples |
| Characteristics |
soil type: upland tundra soil
treatment: 2008 (winter conditions)
sampling depth: top 15 cm
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was co-extracted with RNA from 3 g of soil samples using the MoBio RNA PowerSoil Total RNA Isolation Kit and eluted from the purification column using the RNA PowerSoil DNA Elution Accessory Kit (MoBio Laboratories, Carlsbad, CA)
|
| Label |
Cy5
|
| Label protocol |
Total DNA extracted from all soil samples was submitted to a PCR procedure with eubacterial 16S rRNA gene primers F1-R13, with a touchdown PCR protocol from 65°C to 55°C. PCR products were then chemically labelled using the Label IT nucleic acid labelling kit (Mirus Bio, Madison, WI).
|
| |
|
| Hybridization protocol |
Slides were pre-hybridized for 1 h at 37°C with a DIG easy hybridization solution (Roche Applied Science, Laval, QC, Canada) containing 5% BSA. Samples were then assigned randomly to a sub-array and hybridization was carried out for approximately 20 h at 37°C on a Slide Booster apparatus (Implen, Calabasas, CA). Slides were washed three times for 5 minutes at 37°C in 0.1X SSC / 0.1% SDS followed by a single wash for 5 minutes at 37°C in 0.1X SSC.
|
| Scan protocol |
Slides were scanned in a ScanArray GX PLUS Microarray Scanner (Perkin-Elmer, Boston, MA) at a resolution of 10µm
|
| Data processing |
Spot presence-absence was scored by visual examination of the gridded microarray images. If a spot was visible by eye, it was scored as present (1), if not it was scored as absent (0). For a taxon to be scored as present, all of its triplicate spots had to be scored as present. The results from the 16S rRNA gene microarray were only used in the binary form (presence/absence of taxa).
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| |
|
| Submission date |
Oct 19, 2010 |
| Last update date |
Jan 01, 2011 |
| Contact name |
Martineau Christine |
| E-mail(s) |
christine.martineau@cnrc-nrc.gc.ca
|
| Organization name |
NRC-BRI
|
| Department |
Environmental Microbiology
|
| Street address |
6100 Royalmount Ave.
|
| City |
Montreal |
| State/province |
Qc |
| ZIP/Postal code |
H4P2R2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL8953 |
| Series (1) |
| GSE24800 |
Differences in major bacterial taxa in three high Arctic soils lead to different CO2 production rates |
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