NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM673729 Query DataSets for GSM673729
Status Public on Feb 17, 2011
Title 3519_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: 3519
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: 3519
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_9366102_532
REF_9366102_635
RATIO
EXP_NORM
REF_NORM
VALUE loess normalized log2 test/ref

Data table
ID_REF EXP_9366102_532 REF_9366102_635 RATIO EXP_NORM REF_NORM VALUE
CHR10FS000050315 14.547 14.549 -0.001 14.476 14.607 -0.131
CHR10FS000061607 13.385 12.874 0.511 13.256 13.042 0.214
CHR10FS000098240 13.553 13.527 0.025 13.437 13.637 -0.200
CHR10FS000102028 14.686 14.458 0.228 14.619 14.518 0.100
CHR10FS000118443 14.784 14.694 0.090 14.720 14.747 -0.027
CHR10FS000126471 12.822 12.510 0.312 12.645 12.721 -0.075
CHR10FS000137802 14.637 14.459 0.177 14.568 14.520 0.048
CHR10FS000146265 13.637 13.504 0.133 13.527 13.616 -0.089
CHR10FS000154650 14.298 13.562 0.736 14.217 13.669 0.548
CHR10FS000159386 13.744 13.387 0.357 13.638 13.508 0.130
CHR10FS000166422 12.849 12.054 0.795 12.675 12.335 0.340
CHR10FS000174469 12.518 12.089 0.429 12.305 12.365 -0.060
CHR10FS000179132 13.084 12.533 0.551 12.931 12.741 0.191
CHR10FS000189017 13.805 13.531 0.274 13.704 13.640 0.064
CHR10FS000194652 12.087 12.045 0.041 11.795 12.328 -0.533
CHR10FS000199755 13.707 13.519 0.188 13.600 13.630 -0.029
CHR10FS000210092 13.263 13.033 0.229 13.126 13.184 -0.057
CHR10FS000215810 14.015 13.778 0.237 13.924 13.872 0.052
CHR10FS000220999 13.138 12.665 0.473 12.992 12.856 0.135
CHR10FS000228007 13.276 12.529 0.747 13.141 12.737 0.404

Total number of rows: 385815

Table truncated, full table size 21679 Kbytes.




Supplementary file Size Download File type/resource
GSM673729_3519_Child_Father_532.pair.gz 6.6 Mb (ftp)(http) PAIR
GSM673729_3519_Child_Father_635.pair.gz 6.6 Mb (ftp)(http) PAIR
GSM673729_3519_Father.txt.gz 10.8 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap