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Sample GSM1139169 Query DataSets for GSM1139169
Status Public on Jun 20, 2013
Title Water column DNA_Arabian Sea_Station 3_10m
Sample type mixed
 
Channel 1
Source name Universal Internal Standard + 70-mer
Organism synthetic construct
Characteristics sample type: reference
Extracted molecule other
Extraction protocol DNA was extracted from the filters using the PureGene DNA kit (Gentra, Minneapolis, MN) or the AllPrep DNA/RNA Mini Kit (Qiagen Sciences, Maryland, USA) with slight modifications (as in Ward 2008).
Label Cy5
Label protocol Hybridization targets were prepared by digesting environmental DNA with a four cutter restriction enzyme. The digested environmental DNA were labeled with amino-allyl-dUTP (Ambion) during linear amplification using random octamers and a Klenow polymerase (Applied Biosystems). The reaction contained 3.96 mM d(AGC)TP, 0.44 mM dTTP, and 4.84 mM dUaa and was amplified for 3 h at 37°C. The Klenow product was purified and conjugated with Cy3. The Cy3-labelled target (1000 ng) was combined with 2x hybridization buffer (1x final concentration; Agilent) and 0.25 pmol of a Cy5-labelled complementary 20-mer standard oligonucleotide and incubated at 95°C for 5 min before being cooled to room temperature.
 
Channel 2
Source name Total DNA from water column, Arabian Sea station 3, 10m
Organism marine metagenome
Characteristics location: Arabian Sea Station 3
depth: 10 m
sample type: environmental
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from the filters using the PureGene DNA kit (Gentra, Minneapolis, MN) or the AllPrep DNA/RNA Mini Kit (Qiagen Sciences, Maryland, USA) with slight modifications (as in Ward 2008).
Label Cy3
Label protocol Hybridization targets were prepared by digesting environmental DNA with a four cutter restriction enzyme. The digested environmental DNA were labeled with amino-allyl-dUTP (Ambion) during linear amplification using random octamers and a Klenow polymerase (Applied Biosystems). The reaction contained 3.96 mM d(AGC)TP, 0.44 mM dTTP, and 4.84 mM dUaa and was amplified for 3 h at 37°C. The Klenow product was purified and conjugated with Cy3. The Cy3-labelled target (1000 ng) was combined with 2x hybridization buffer (1x final concentration; Agilent) and 0.25 pmol of a Cy5-labelled complementary 20-mer standard oligonucleotide and incubated at 95°C for 5 min before being cooled to room temperature.
 
 
Hybridization protocol Samples were hybridized to duplicate arrays by overnight incubation at 64°C and washed.
Scan protocol The arrays were scanned with a laser scanner (Molecular Devices 4200).
Images were analyzed with GenePix Pro 6.0 software (Molecular Devices).
Description AS3.10m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.
Data processing Quality control was employed to remove noise by eliminating features 1) in which the Cy3 signal was not at least twice the value of the control probes, and 2) in which the Cy3/Cy5 could not pass a Z test to find out the outlier values. The Z test was performed by calculating Zi = ri/(s/square root of 3), i = 1, 2, or 3, where ri represents Cy3/Cy5, s the standard deviation of the triplicate Cy3/Cy5 values. A feature is considered as an outlier if the Z is greater than 1.9 (CI = 80%).
Cy3/Cy5 fluorescence intensities were standardized to the highest Cy3/Cy5 fluorescence across the AOA probe set (normalized fluorescence ratio; FRN).
 
Submission date May 12, 2013
Last update date Jun 20, 2013
Contact name Xuefeng Peng
Organization name Princeton University
Department Geosciences
Street address Guyot Hall
City Princeton
State/province NJ
ZIP/Postal code 08544
Country USA
 
Platform ID GPL17151
Series (1)
GSE46851 Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones

Data table header descriptions
ID_REF
VALUE Log2 normalized Cy3/C5 ratio
PRE_VALUE Normalized Cy3/C5 ratio

Data table
ID_REF VALUE PRE_VALUE
AOA1 -3.5907 0.083
AOA2 -4.7959 0.036
AOA3 -1.8836 0.271
AOA4 -0.1297 0.914
AOA5 -4.8783 0.034
AOA6 -5.0116 0.031
AOA7 -3.1078 0.116
AOA8 -2.8059 0.143
AOA9 -1.4501 0.366
AOA10 -2.3004 0.203
AOA11 -3.2243 0.107
AOA12 -1.8890 0.270
AOA13 -2.1078 0.232
AOA14 -3.6439 0.080
AOA15 -2.6804 0.156
AOA16 -4.2653 0.052
AOA17 0.0000 1.000
AOA18 -1.4189 0.374
AOA19 -0.9159 0.530
AOA20 -3.2793 0.103

Total number of rows: 31

Table truncated, full table size <1 Kbytes.




Supplementary file Size Download File type/resource
GSM1139169_BC014-20-1_Irregular.gpr.gz 147.8 Kb (ftp)(http) GPR
GSM1139169_BC014-20-2_Irregular.gpr.gz 146.9 Kb (ftp)(http) GPR
GSM1139169_BC014_20_1NewFilterS-Irbbw.xlsx.gz 716.3 Kb (ftp)(http) XLSX
GSM1139169_BC014_20_2NewFilterS-Irbbw.xlsx.gz 724.0 Kb (ftp)(http) XLSX
Processed data included within Sample table
Processed data provided as supplementary file

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