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Sample GSM673735 Query DataSets for GSM673735
Status Public on Feb 17, 2011
Title 5993_Child_Father (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: 5993
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: 5993
family member: Father
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_4833302_532
REF_4833302_635
RATIO
EXP_NORM
REF_NORM
VALUE loess normalized log2 test/ref

Data table
ID_REF EXP_4833302_532 REF_4833302_635 RATIO EXP_NORM REF_NORM VALUE
CHR10FS000050315 13.438 13.466 -0.028 13.359 13.536 -0.177
CHR10FS000061607 12.242 12.071 0.170 12.107 12.217 -0.110
CHR10FS000098240 12.534 12.505 0.029 12.418 12.618 -0.200
CHR10FS000102028 13.767 13.509 0.258 13.698 13.576 0.122
CHR10FS000118443 14.307 13.946 0.361 14.244 13.999 0.244
CHR10FS000126471 11.818 10.951 0.868 11.643 11.210 0.433
CHR10FS000137802 12.322 12.172 0.150 12.193 12.309 -0.116
CHR10FS000146265 12.499 12.494 0.004 12.380 12.608 -0.228
CHR10FS000154650 12.580 12.581 -0.001 12.466 12.689 -0.223
CHR10FS000159386 12.342 12.089 0.253 12.213 12.232 -0.019
CHR10FS000166422 12.182 11.960 0.223 12.043 12.114 -0.071
CHR10FS000174469 11.844 11.606 0.238 11.673 11.797 -0.124
CHR10FS000179132 12.288 11.999 0.289 12.156 12.150 0.007
CHR10FS000189017 12.408 12.069 0.339 12.284 12.215 0.070
CHR10FS000194652 11.397 10.801 0.596 11.202 11.085 0.117
CHR10FS000199755 12.474 12.297 0.178 12.354 12.424 -0.070
CHR10FS000210092 12.305 11.889 0.416 12.174 12.049 0.125
CHR10FS000215810 12.305 12.177 0.128 12.174 12.313 -0.139
CHR10FS000220999 12.760 12.532 0.228 12.656 12.643 0.012
CHR10FS000228007 12.121 11.732 0.389 11.978 11.910 0.068

Total number of rows: 385815

Table truncated, full table size 21662 Kbytes.




Supplementary file Size Download File type/resource
GSM673735_5993_Child_Father_532.pair.gz 6.5 Mb (ftp)(http) PAIR
GSM673735_5993_Child_Father_635.pair.gz 6.5 Mb (ftp)(http) PAIR
GSM673735_5993_Father.txt.gz 10.8 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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