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Sample GSM673718 Query DataSets for GSM673718
Status Public on Feb 17, 2011
Title 2332_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: 2332
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: 2332
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_3792602_532
REF_3792602_635
RATIO
EXP_NORM
REF_NORM
VALUE loess normalized log2 test/ref

Data table
ID_REF EXP_3792602_532 REF_3792602_635 RATIO EXP_NORM REF_NORM VALUE
CHR10FS000050315 14.202 14.308 -0.107 14.178 14.304 -0.125
CHR10FS000061607 13.817 13.458 0.359 13.747 13.554 0.193
CHR10FS000098240 13.515 13.382 0.133 13.401 13.488 -0.087
CHR10FS000102028 14.326 14.374 -0.048 14.314 14.364 -0.050
CHR10FS000118443 14.615 14.683 -0.068 14.629 14.644 -0.015
CHR10FS000126471 12.851 12.237 0.614 12.596 12.574 0.021
CHR10FS000137802 12.672 11.905 0.767 12.364 12.336 0.028
CHR10FS000146265 13.195 12.875 0.320 13.022 13.067 -0.045
CHR10FS000154650 13.197 12.960 0.237 13.025 13.136 -0.111
CHR10FS000159386 13.067 12.701 0.366 12.866 12.927 -0.061
CHR10FS000166422 13.253 12.931 0.322 13.091 13.113 -0.022
CHR10FS000174469 12.587 11.900 0.687 12.253 12.333 -0.080
CHR10FS000179132 13.277 12.796 0.481 13.120 13.004 0.115
CHR10FS000189017 13.403 13.268 0.135 13.271 13.391 -0.120
CHR10FS000194652 12.444 11.218 1.227 12.055 11.902 0.153
CHR10FS000199755 13.241 12.965 0.277 13.077 13.140 -0.063
CHR10FS000210092 13.009 12.458 0.552 12.795 12.740 0.055
CHR10FS000215810 13.302 13.274 0.028 13.149 13.396 -0.246
CHR10FS000220999 13.677 13.063 0.613 13.586 13.220 0.366
CHR10FS000228007 13.289 12.898 0.391 13.133 13.085 0.048

Total number of rows: 385815

Table truncated, full table size 21679 Kbytes.




Supplementary file Size Download File type/resource
GSM673718_2332_Child_Mother_532.pair.gz 6.6 Mb (ftp)(http) PAIR
GSM673718_2332_Child_Mother_635.pair.gz 6.6 Mb (ftp)(http) PAIR
GSM673718_2332_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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