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Series GSE42286 Query DataSets for GSE42286
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
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
 
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.
 
Contributor(s) Newell S, Ward B
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Nov 14, 2012
Last update date Mar 03, 2013
Contact name Silvia Newell
E-mail(s) sen@bu.edu
Organization name Boston University
Street address 675 Commonwealth Ave.
City Boston
State/province Massachusetts
ZIP/Postal code 02215
Country USA
 
Platforms (1)
GPL16281 Princeton Microarray Facility AOA Archetype Microarray BC014
Samples (15)
GSM1037125 Control site sediment DNA [CT July 2008]
GSM1037126 Control site sediment DNA [CT Sept 2008]
GSM1037127 Control site sediment DNA [CT Jan 2009]
Relations
BioProject PRJNA179549

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
GSE42286_RAW.tar 8.2 Mb (http)(custom) TAR (of GPR, TXT)
Processed data included within Sample table

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