GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE3264 Query DataSets for GSE3264
Status Public on Dec 19, 2005
Title Oligonucleotide-based arrayCGH
Organisms Homo sapiens; Mus musculus
Experiment type Genome variation profiling by array
Genome variation profiling by genome tiling array
Summary Array-based comparative genomic hybridisation is a high-resolution method for measuring chromosomal copy number changes. Here we present a validated protocol using in-house spotted oligonucleotide libraries for array CGH. This oligo array CGH platform yields reproducible results and is capable of detecting single copy gains, multi-copy amplifications as well as homozygous and heterozygous deletions as small as 100 kb with high resolution. A human oligonucleotide library was printed on amine binding slides. Arrays were hybridised using a hybstation and analysed using BleuFuse feature extraction software, with over 95% of spots passing quality control. The protocol allows as little as 300 ng of input DNA without the need for amplification or target reduction and a 90% reduction of Cot1-DNA without compromising quality. High quality results have also been obtained with DNA from archival tissue. Finally, in addition to human oligo arrays, we have applied the protocol successfully to mouse oligo arrays. We believe that this oligo-based platform using “off-the-shelf” oligo-libraries provides an easy accessible alternative to BAC arrays for CGH, which is cost-effective, available at high resolution and easily implemented for any sequenced organism without compromising the quality of the results.
Keywords: comparative genomic hybridization, oligonucleotide,
Overall design 16 human and 2 mouse samples are analyzed on oligonucleotide arrays and some of them also on BAC arrays. Replicates are included in the series so that the total number of hybridizations is 30. Corresponding figure numbers: 1A/C: GSM73557, 1B/D: GSM75163, 2: GSM74521, 3: GSM73557, GSM75164, GSM75165, GSM75166, 4A: GSM75169, 4C: GSM75170, 5A: GSM75171, 6A: GSM75199, 6B: GSM75205, 7A: GSM75209, 7B: GSM75175, GSM75174.
Contributor(s) van den IJssel P, Tijssen M, Chin S, Eijk PP, Carvalho B, Hopmans E, Holstege H, Jonkers J, Meijer GA, Caldas C, Ylstra B
Citation(s) 16361265
Submission date Sep 08, 2005
Last update date Aug 08, 2013
Contact name Daoud Sie
Phone +31 20 4442428
Organization name Vrije Universiteit Medical Center
Department Pathology
Lab Microarray Core Facility
Street address De Boelelaan 1117
City Amsterdam
ZIP/Postal code 1081 HV
Country Netherlands
Platforms (11)
GPL2819 VUMC MACF human 30K oligo v42
GPL2826 VUMC MACF human 30K oligo v31
GPL2827 VUMC MACF human 30K oligo v44
Samples (36)
GSM73557 BT474 (ATCC nr. HTB-20) Breast tumor cell line BT474_b42_s56
GSM74521 GM01750_b42_s51
GSM74522 GM13031_b42_s54
BioProject PRJNA92921

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

Supplementary data files not provided

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