|
| Status |
Public on Feb 17, 2011 |
| Title |
2894_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: 2894
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: 2894
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 |
|
