NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM501717 Query DataSets for GSM501717
Status Public on Mar 08, 2010
Title Active layer
Sample type genomic
 
Source name Eureka
Organism environmental samples
Characteristics year: 2003
sample type: Active layer soil
sample name: A
source: overlying active layer soil of 2M
Extracted molecule genomic DNA
Extraction protocol Soil DNA was extracted from a 10 g soil sub-sample using the MoBio PowerMax Soil DNA Isolation 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 an annealing temperature of 50°C. RT-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
Description n/a
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).
 
Submission date Jan 27, 2010
Last update date Mar 08, 2010
Contact name Etienne Yergeau
E-mail(s) Etienne.Yergeau@cnrc-nrc.gc.ca
Organization name NRC-BRI
Department Environmental Microbiology
Street address 6100 Royalmount Ave
City Montreal
State/province Qc
ZIP/Postal code H4P 2R2
Country Canada
 
Platform ID GPL8953
Series (1)
GSE20073 The functional potential of high Arctic permafrost

Data table header descriptions
ID_REF
VALUE Binary (presence=1, absence=0)

Data table
ID_REF VALUE
25_EUB338 1
DQ628943.1 1
DQ522907.1 1
EU045047.1 0
EU044950.1 0
EF200116.1 0
EF069362.1 1
Psychrobacter 0
DQ628961.1 0
DQ522910.1 0
DQ521379.1 0
EU045065.1 0
EU044951.1 0
EU030489.1 0
EF069374.1 0
Pseudomonas 1
DQ640135.1 0
DQ522930.1 0
DQ521493.1 0
EU045076.1 0

Total number of rows: 160

Table truncated, full table size 2 Kbytes.




Supplementary file Size Download File type/resource
GSM501717_Sample2M.txt.gz 23.8 Kb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap