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Status |
Public on Mar 01, 2013 |
Title |
Ammonia oxidizing archaeal community composition in Gulf of Mexico sediments investigated with an amoA functional gene microarray |
Platform organism |
synthetic construct |
Sample organisms |
synthetic construct; uncultured ammonia-oxidizing archaeon |
Experiment type |
Other
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Summary |
Ammonia-oxidizing archaeal (AOA) amoA diversity and relative abundance in Gulf of Mexico sediments (0-2 cm) were investigated using a functional gene microarray; a two color array with a universal internal standard
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Overall design |
Two color array (cy3 and cy5): the universal standard 20 bp oligo (fluoresced with cy5) is printed to the slide with a 70-mer. Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer will bind to it. Signal is the cy3/cy5. Up to four arrays per sample, with two biological replicates made into two targets, each run on duplicate arrays.
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Contributor(s) |
Newell S, Ward B |
Citation missing |
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Submission date |
Nov 14, 2012 |
Last update date |
Mar 03, 2013 |
Contact name |
Silvia Newell |
E-mail(s) |
sen@bu.edu
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Organization name |
Boston University
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Street address |
675 Commonwealth Ave.
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City |
Boston |
State/province |
Massachusetts |
ZIP/Postal code |
02215 |
Country |
USA |
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Platforms (1) |
GPL16281 |
Princeton Microarray Facility AOA Archetype Microarray BC014 |
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Samples (15)
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GSM1037125 |
Control site sediment DNA [CT July 2008] |
GSM1037126 |
Control site sediment DNA [CT Sept 2008] |
GSM1037127 |
Control site sediment DNA [CT Jan 2009] |
GSM1037128 |
Control site sediment DNA [CT Aug 2009] |
GSM1037129 |
Control site sediment DNA [CT May 2010] |
GSM1037130 |
Control site sediment DNA [CT Aug 2010] |
GSM1037131 |
Control site sediment DNA [CT May 2011] |
GSM1037132 |
Deepwater Horizon site sediment DNA [DWH May 2011-1] |
GSM1037133 |
C6 site sediment DNA [C6 July 2008] |
GSM1037134 |
C6 site sediment DNA [C6 Sept 2008] |
GSM1037135 |
C6 site sediment DNA [C6 Jan 2009] |
GSM1037136 |
C6 site sediment DNA [C6 May 2010] |
GSM1037137 |
C6 site sediment DNA [C6 Aug 2010] |
GSM1037138 |
C6 site sediment DNA [C6 May 2011] |
GSM1037139 |
Deepwater Horizon site sediment DNA [DWH May 2011-2] |
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Relations |
BioProject |
PRJNA179549 |