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| Status |
Public on Nov 18, 2006 |
| Title |
Efficient High-Resolution Discovery in C. elegans by Array Comparative Genomic Hybridization |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Genome variation profiling by genome tiling array
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| Summary |
The Males Experiment:
This experiment was done to test the sensitivity of our array in detecting single copy losses of probes to the X chromosome. Males (XO) have just one X chromosome, while hermaphrodites (XX) have two.
CB4856 and JU258:
This experiment was done to determine the natural copy number variation that exists in a wild C. elegans isolate. Extensive natural copy number variation exists in this strain.
gkDf2 (VC100):
This control experiment was done to confirm that we could reliably detect a large 50-kb homozygous deletion on chromosome X using this array.
gk329 (VC766):
This control experiment was done to confirm that we could reliably detect a homozygous 1-kb single-gene deletion on the X chromosome. This deletion targets the gene ceh-39.
For gk291 (VC615):
This control experiment was done to confirm that we could reliably detect a heterozygous (single copy) single-gene 1-kb deletion on chromsome II. This deletion targets the gene dab-1.
All other experiments:
This experiment was done in an effort to detect novel balanced single copy losses on chromosome II in mutagenized strains. Mutants were previously screened for homozygous lethal mutations on chromosome II, and these mutations were then balanced with the mIn1 balancer chromosome to generate the mutant strain screened in this experiment.
Keywords: comparative genomic hybridization
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| Overall design |
This is a simple Test vs. Reference CGH experiment. One test sample was cohybridized with a reference sample (the strain N2). There were no replicates or dye-swaps performed.
For each forward probe on the X:II chip there is also a probe with the reverse complement sequence.
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| Citation(s) |
17267812 |
| |
| Submission date |
Nov 15, 2006 |
| Last update date |
Mar 17, 2012 |
| Contact name |
Donald Moerman |
| Organization name |
University of British Columbia
|
| Department |
Michael Smith Laboratories
|
| Street address |
301 - 2185 East Mall
|
| City |
Vancouver |
| State/province |
British Columbia |
| ZIP/Postal code |
V6T 1Z4 |
| Country |
Canada |
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| Platforms (3) |
| GPL4551 |
Array designs: Chromosomes X and II |
| GPL4552 |
Array designs: Chromosome II |
| GPL4553 |
Array designs: Whole Genome |
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| Samples (14)
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| Relations |
| BioProject |
PRJNA100607 |
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