Abstract:
:The genomic instability of stem cells in culture, caused by their routine in vitro propagation or by their genetic manipulation, is deleterious both for their clinical application and for their use in basic research. Frequent evaluation of the genomic integrity of stem cells is thus required, and it is usually performed using cytogenetic or DNA-based methods at variable sensitivities, resolutions and costs. Here we present a detailed protocol for determining the genomic integrity of pluripotent stem cells (PSCs) using their global gene expression profiles. This expression-based karyotyping (e-karyotyping) protocol uses gene expression microarray data (either originally generated or derived from the literature) and describes how to organize it properly, subject it to two complementary bioinformatic analyses and conservatively interpret the results in order to generate an accurate estimation of the chromosomal aberrations in the autosomal genome of examined stem cell lines. The experimental steps of e-karyotyping can be carried out in ∼20-30 h.
journal_name
Nat Protocjournal_title
Nature protocolsauthors
Ben-David U,Mayshar Y,Benvenisty Ndoi
10.1038/nprot.2013.051subject
Has Abstractpub_date
2013-05-01 00:00:00pages
989-97issue
5eissn
1754-2189issn
1750-2799pii
nprot.2013.051journal_volume
8pub_type
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