E-GEOD-8567 - Genotyping of human cell lines with amplification of single cell vs. non amplied products to examime the effect of allele bias during amplification

Status
Submitted on 23 July 2007, released on 16 June 2008, last updated on 2 May 2014
Organism
Homo sapiens
Samples (17)
Array (1)
Protocols (5)
Description
Single-cell human genome analysis using whole-genome amplified product is hampered by allele bias during amplification. Using an oligonucleotide SNP array, we examined the nature of the allele bias and its effect on the chromosomal copy number analysis. Experiment Overall Design: TB106, lymphoblastoid cell line; CMK11-5 and CMK86, cell line; WGA, whole-genome amplified from bulk DNA; SC, whole-genome amplified product from single cell. Genotype and copy number status were compared between non-amplified products and their single cell products.
Experiment types
genotyping by array, unknown experiment type
Contact
Citation
Detection of chromosomal structural alterations in single cells by SNP arrays: a systematic survey of amplification bias and optimized workflow. Kazuya Iwamoto, Miki Bundo, Junko Ueda, Yoko Nakano, Wataru Ukai, Eri Hashimoto, Toshikazu Saito, Tadafumi Kato. PLoS ONE 2(12):e1306 (2007)
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-8567.idf.txt
Sample and data relationshipE-GEOD-8567.sdrf.txt
Raw data (3)E-GEOD-8567.raw.1.zip, E-GEOD-8567.raw.2.zip, E-GEOD-8567.raw.3.zip
Processed data (1)E-GEOD-8567.processed.1.zip
Array designA-AFFY-70.adf.txt
R ExpressionSetE-GEOD-8567.eSet.r
Links