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Series GSE9002 Query DataSets for GSE9002
Status Public on Sep 28, 2007
Title 8-chip high-resolution aCGH experiment NA15510 vs. NA18505
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary We introduce high-throughput and massive paired-end mapping (PEM), a large-scale genome sequencing method to identify SVs 3 kb or larger that combines the rescue and capture of paired-ends of 3 kb fragments, massive 454 Sequencing, and a computational approach to map DNA reads onto a reference genome. PEM was used to map SVs in an African and putatively European individual and identified shared and divergent SVs relative to the reference genome. Overall, we fine-mapped more than 1000 SVs and documented that the number of SVs among humans is much larger than initially hypothesized; many of the SVs potentially affect gene function. The breakpoint junction sequences of more than 200 SVs were deduced with a novel pooling strategy and computational analysis. Array-CGH was used for validation.
Keywords: array CGH
Overall design 2 samples were analyzed with 8 different Nimblegen chips (385k); thus ~30M probes were used to interrogate copy number variants in NA15510 (using NA18505 as control) at high resolution.
Contributor(s) Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero N, Du L, Taillon B, Tanzer A, Saunders E, Chi J, Yang F, Carter N, Hurles M, Weissman S, Harkins TT, Gerstein MB, Egholm M, Snyder M, Chen Z
Citation(s) 17901297
Submission date Sep 10, 2007
Last update date Mar 17, 2012
Contact name Jan Oliver Korbel
Phone +1 203 432 5405
Fax +1 203 432 5175
Organization name Yale University
Street address 266 Whitney Avenue
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
Platforms (8)
GPL5814 NimbleGen Homo sapiens HG18 Whole Genome CGH Tiling Set (1 of 8)
GPL5815 NimbleGen Homo sapiens HG18 Whole Genome CGH Tiling Set (2 of 8)
GPL5816 NimbleGen Homo sapiens HG18 Whole Genome CGH Tiling Set (3 of 8)
Samples (8)
GSM227608 CGH WG-set_1of8 NA18505 vs. NA15510
GSM228515 CGH WG-set_2of8 NA18505 vs. NA15510
GSM228516 CGH WG-set_3of8 NA18505 vs. NA15510
BioProject PRJNA102481

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE9002_RAW.tar 287.1 Mb (http)(custom) TAR (of PAIR)
Processed data included within Sample table

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