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Sample GSM673231 Query DataSets for GSM673231
Status Public on Feb 17, 2011
Title 8612_Child_Father (Agilent 244K)
Sample type genomic
 
Channel 1
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
tissue: peripheral blood
family: 8612
family member: Child
phenotype: idiopathic MR
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from blood samples using the Puregene DNA kit
Label Cy3
Label protocol 3 μg of high-quality genomic DNA were digested with RsaI and AluI and labeled with Cyanine-3 or Cyanine-5 using a random priming method. Two arrays were used for each trio, one in which the child’s DNA was hybridized against the father’s DNA, and another in which the child’s DNA was hybridized against the mother’s DNA. Equal amounts of the child’s and one parent’s DNA were labeled with opposite fluorochromes and hybridized to the array
 
Channel 2
Source name peripheral blood
Organism Homo sapiens
Characteristics family: 8612
family member: Father
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from blood samples using the Puregene DNA kit
Label Cy5
Label protocol 3 μg of high-quality genomic DNA were digested with RsaI and AluI and labeled with Cyanine-3 or Cyanine-5 using a random priming method. Two arrays were used for each trio, one in which the child’s DNA was hybridized against the father’s DNA, and another in which the child’s DNA was hybridized against the mother’s DNA. Equal amounts of the child’s and one parent’s DNA were labeled with opposite fluorochromes and hybridized to the array
 
 
Hybridization protocol 3 day hyb at 65C in Agilent Hyb Oven
Scan protocol 5um scan with Agilent Scanner and Agilent Scanner Control Software v7.0
Data processing Captured images were analysed with Feature Extraction v 9.1 and CGH Analytics 3.5.14 using the ADM-1 algorithm to identify regions with consistently high or low log2 ratio. This algorithm does not rely on a window size but rather samples immediately adjacent probes and uses the average normalized log2 ratios of all probes in a genomic interval to determine the deviation of the log2 ratio from its expected value of zero. A user-defined stringency threshold of 6, the recommended default value, was set. Two other methods were also used to assist in the aberration calls. A centralization process was performed that assumes the log2 ratio values are centered at zero and re-centers the data by finding a constant value to add to or subtract from all log2 values. The program uses a default of a 10 probe window to average the log2 ratios. Also, a “fuzzy zero” method, which applies a global error mode to all aberrant intervals identified by the ADM-1 algorithm, was used to avoid erroneous aberration calls when the errors were correlated.
 
Submission date Feb 10, 2011
Last update date Feb 17, 2011
Contact name Tracy Tucker
E-mail(s) tbtucker@interchange.ubc.ca
Organization name University of British Columbia
Street address Box 153 4480 Oak Street
City Vancouver
ZIP/Postal code V6H3V4
Country Canada
 
Platform ID GPL4091
Series (2)
GSE27229 Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR (Agilent 244K)
GSE27367 Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 -2.417536267e-002
2 -8.932420815e-002
3 0.000000000e+000
4 3.490227185e-002
5 -5.923993461e-002
6 -5.457857708e-002
7 -3.902182643e-003
8 -4.591058314e-003
9 -7.491181743e-003
10 2.594056365e-001
11 -1.929525433e-001
12 5.438969150e-002
13 -4.042039436e-002
14 -4.863355752e-002
15 5.334652244e-003
16 -8.941128831e-002
17 1.647994444e-002
18 -1.176441034e+000
19 -6.552446235e-002
20 1.016228729e-001

Total number of rows: 243430

Table truncated, full table size 5721 Kbytes.




Supplementary file Size Download File type/resource
GSM673231_8612_Father.txt.gz 66.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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