NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM673730 Query DataSets for GSM673730
Status Public on Feb 17, 2011
Title 3519_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: 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: 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_9353902_532
REF_9353902_635
RATIO
EXP_NORM
REF_NORM
VALUE loess normalized log2 test/ref

Data table
ID_REF EXP_9353902_532 REF_9353902_635 RATIO EXP_NORM REF_NORM VALUE
CHR10FS000050315 13.278 13.198 0.080 13.186 13.269 -0.083
CHR10FS000061607 11.455 10.969 0.486 11.235 11.257 -0.022
CHR10FS000098240 12.251 11.491 0.760 12.108 11.707 0.401
CHR10FS000102028 13.038 12.694 0.344 12.940 12.793 0.147
CHR10FS000118443 13.492 13.150 0.341 13.408 13.224 0.184
CHR10FS000126471 11.555 10.968 0.587 11.346 11.257 0.089
CHR10FS000137802 13.250 12.855 0.394 13.157 12.944 0.213
CHR10FS000146265 12.360 12.133 0.227 12.224 12.274 -0.050
CHR10FS000154650 12.784 11.963 0.821 12.674 12.122 0.552
CHR10FS000159386 11.842 11.742 0.100 11.653 11.922 -0.269
CHR10FS000166422 11.795 11.522 0.273 11.600 11.735 -0.135
CHR10FS000174469 11.168 10.577 0.591 10.906 10.942 -0.037
CHR10FS000179132 11.605 11.211 0.394 11.399 11.467 -0.069
CHR10FS000189017 12.263 12.318 -0.055 12.121 12.443 -0.322
CHR10FS000194652 11.093 10.308 0.785 10.819 10.740 0.079
CHR10FS000199755 12.375 11.974 0.401 12.239 12.131 0.108
CHR10FS000210092 12.002 11.731 0.271 11.832 11.912 -0.081
CHR10FS000215810 12.592 12.214 0.378 12.472 12.349 0.123
CHR10FS000220999 11.840 11.231 0.609 11.651 11.484 0.167
CHR10FS000228007 11.329 10.942 0.387 11.092 11.234 -0.142

Total number of rows: 385815

Table truncated, full table size 21646 Kbytes.




Supplementary file Size Download File type/resource
GSM673730_3519_Child_Mother_532.pair.gz 6.5 Mb (ftp)(http) PAIR
GSM673730_3519_Child_Mother_635.pair.gz 6.5 Mb (ftp)(http) PAIR
GSM673730_3519_Mother.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