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Sample GSM673766 Query DataSets for GSM673766
Status Public on Feb 17, 2011
Title 9390_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: 9390
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: 9390
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_3240502_532
REF_3240502_635
RATIO
EXP_NORM
REF_NORM
VALUE loess normalized log2 test/ref

Data table
ID_REF EXP_3240502_532 REF_3240502_635 RATIO EXP_NORM REF_NORM VALUE
CHR10FS000050315 13.699 13.701 -0.002 13.642 13.722 -0.080
CHR10FS000061607 11.683 11.803 -0.120 11.569 11.921 -0.352
CHR10FS000098240 11.951 11.038 0.913 11.866 11.274 0.592
CHR10FS000102028 13.394 12.834 0.561 13.340 12.871 0.469
CHR10FS000118443 13.046 12.820 0.225 12.993 12.859 0.134
CHR10FS000126471 12.079 11.628 0.451 12.003 11.768 0.235
CHR10FS000137802 13.538 13.171 0.367 13.483 13.198 0.285
CHR10FS000146265 12.511 12.689 -0.178 12.454 12.732 -0.277
CHR10FS000154650 13.070 12.950 0.120 13.017 12.981 0.035
CHR10FS000159386 12.419 11.955 0.464 12.360 12.056 0.304
CHR10FS000166422 11.772 11.758 0.014 11.668 11.881 -0.214
CHR10FS000174469 11.399 11.281 0.118 11.254 11.479 -0.225
CHR10FS000179132 11.804 11.288 0.517 11.703 11.484 0.219
CHR10FS000189017 12.641 12.159 0.482 12.587 12.241 0.347
CHR10FS000194652 11.663 11.209 0.454 11.547 11.417 0.130
CHR10FS000199755 12.259 12.002 0.257 12.193 12.098 0.095
CHR10FS000210092 12.102 11.803 0.300 12.028 11.921 0.106
CHR10FS000215810 12.297 11.201 1.096 12.233 11.411 0.822
CHR10FS000220999 11.948 11.984 -0.037 11.862 12.082 -0.220
CHR10FS000228007 11.420 12.135 -0.715 11.278 12.219 -0.941

Total number of rows: 385815

Table truncated, full table size 21742 Kbytes.




Supplementary file Size Download File type/resource
GSM673766_9390_Child_Mother_532.pair.gz 6.5 Mb (ftp)(http) PAIR
GSM673766_9390_Child_Mother_635.pair.gz 6.5 Mb (ftp)(http) PAIR
GSM673766_9390_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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