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Sample GSM673732 Query DataSets for GSM673732
Status Public on Feb 17, 2011
Title 3921_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: 3921
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: 3921
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_3210602_532
REF_3210602_635
RATIO
EXP_NORM
REF_NORM
VALUE loess normalized log2 test/ref

Data table
ID_REF EXP_3210602_532 REF_3210602_635 RATIO EXP_NORM REF_NORM VALUE
CHR10FS000050315 13.190 13.517 -0.327 13.425 13.289 0.136
CHR10FS000061607 11.838 12.323 -0.485 12.047 12.142 -0.096
CHR10FS000098240 11.930 12.198 -0.269 12.142 12.025 0.116
CHR10FS000102028 13.079 13.300 -0.221 13.318 13.080 0.238
CHR10FS000118443 12.563 12.971 -0.408 12.798 12.760 0.038
CHR10FS000126471 11.543 11.391 0.152 11.742 11.289 0.453
CHR10FS000137802 11.483 12.034 -0.551 11.680 11.869 -0.190
CHR10FS000146265 11.903 12.495 -0.593 12.114 12.306 -0.192
CHR10FS000154650 11.846 12.229 -0.383 12.056 12.054 0.001
CHR10FS000159386 12.121 12.645 -0.523 12.341 12.448 -0.107
CHR10FS000166422 11.763 12.491 -0.728 11.969 12.302 -0.333
CHR10FS000174469 10.980 11.648 -0.668 11.120 11.517 -0.396
CHR10FS000179132 11.705 12.134 -0.428 11.909 11.964 -0.055
CHR10FS000189017 12.524 12.691 -0.167 12.759 12.492 0.267
CHR10FS000194652 11.087 11.263 -0.175 11.242 11.177 0.065
CHR10FS000199755 11.989 12.262 -0.273 12.204 12.086 0.119
CHR10FS000210092 11.404 11.847 -0.442 11.595 11.695 -0.100
CHR10FS000215810 12.409 12.840 -0.432 12.639 12.634 0.005
CHR10FS000220999 12.089 12.970 -0.882 12.309 12.760 -0.451
CHR10FS000228007 11.376 11.863 -0.487 11.564 11.710 -0.146

Total number of rows: 385815

Table truncated, full table size 21963 Kbytes.




Supplementary file Size Download File type/resource
GSM673732_3921_Child_Mother_532.pair.gz 6.5 Mb (ftp)(http) PAIR
GSM673732_3921_Child_Mother_635.pair.gz 6.5 Mb (ftp)(http) PAIR
GSM673732_3921_Mother.txt.gz 10.9 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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