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Sample GSM673768 Query DataSets for GSM673768
Status Public on Feb 17, 2011
Title 9609_Child_Mother (NimbleGen)
Sample type genomic
 
Channel 1
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
tissue: peripheral blood
phenotype: idiopathic MR
family: 9609
family member: Child
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from blood samples using the Puregene DNA kit
Label Cy5
Label protocol DNA was sent to NimbleGen Systems, Inc. (Reykjavik, Iceland), where the hybridizations were performed.
 
Channel 2
Source name peripheral blood
Organism Homo sapiens
Characteristics tissue: peripheral blood
phenotype: unaffected
family: 9609
family member: Mother
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from blood samples using the Puregene DNA kit
Label Cy3
Label protocol DNA was sent to NimbleGen Systems, Inc. (Reykjavik, Iceland), where the hybridizations were performed.
 
 
Hybridization protocol 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
Scan protocol The arrays were scanned at 5µm resolution on a GenePix 4000B Scanner.
Data processing Data from the hybridizations were analyzed using NimbleScan version 2.4.1 segMNT algorithm
Parameters: 1) the minimum segment difference, which represents the minimum difference in the log2 ratio that two segments must exhibit before they are identified as separate segments, was set at 0.0; 2) the minimum segment length, which represents the minimum number of consecutive probes that must exhibit a change in log2 ratio in order to call a segment, was set at 2; and 3) the acceptance percentile, which represents the stringency with which initial segment boundaries are selected, was set at 0.999. Only segments with a mean absolute log2 ratio of 0.2 or more were considered for further analysis.
 
Submission date Feb 11, 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 GPL7717
Series (2)
GSE27251 Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR (NimbleGen)
GSE27367 Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR

Data table header descriptions
ID_REF
EXP_3309402_532
REF_3309402_635
RATIO
EXP_NORM
REF_NORM
VALUE loess normalized log2 test/ref

Data table
ID_REF EXP_3309402_532 REF_3309402_635 RATIO EXP_NORM REF_NORM VALUE
CHR10FS000050315 14.413 14.521 -0.108 14.426 14.474 -0.048
CHR10FS000061607 12.507 12.829 -0.322 12.485 12.846 -0.361
CHR10FS000098240 13.568 13.055 0.512 13.579 13.059 0.520
CHR10FS000102028 13.806 13.802 0.003 13.819 13.774 0.045
CHR10FS000118443 14.545 14.485 0.060 14.559 14.440 0.119
CHR10FS000126471 12.500 12.215 0.286 12.478 12.288 0.191
CHR10FS000137802 13.025 12.884 0.141 13.024 12.897 0.126
CHR10FS000146265 13.012 13.374 -0.362 13.010 13.362 -0.352
CHR10FS000154650 13.987 13.965 0.022 14.003 13.933 0.070
CHR10FS000159386 12.490 13.045 -0.555 12.468 13.049 -0.582
CHR10FS000166422 13.141 12.830 0.311 13.143 12.848 0.295
CHR10FS000174469 12.190 12.524 -0.334 12.143 12.565 -0.422
CHR10FS000179132 13.003 12.730 0.272 13.000 12.755 0.246
CHR10FS000189017 13.145 12.870 0.275 13.146 12.884 0.263
CHR10FS000194652 11.376 11.422 -0.046 11.227 11.630 -0.403
CHR10FS000199755 12.966 13.090 -0.124 12.962 13.092 -0.130
CHR10FS000210092 12.686 12.648 0.037 12.671 12.679 -0.007
CHR10FS000215810 13.368 13.045 0.323 13.375 13.050 0.325
CHR10FS000220999 12.821 12.792 0.029 12.813 12.812 0.001
CHR10FS000228007 12.483 12.745 -0.262 12.460 12.769 -0.309

Total number of rows: 385815

Table truncated, full table size 21792 Kbytes.




Supplementary file Size Download File type/resource
GSM673768_9609_Child_Mother_532.pair.gz 6.6 Mb (ftp)(http) PAIR
GSM673768_9609_Child_Mother_635.pair.gz 6.6 Mb (ftp)(http) PAIR
GSM673768_9609_Mother.txt.gz 10.8 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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