Genome-wide copy number profiling of mouse neural stem cells during differentiation.
There is growing evidence that gene amplifications were present in neural stem and progenitor cells during differentiation. We used array-CGH to discover copy number changes including gene amplifications and deletions during differentiation of mouse neural stem cells using TGF-ß and FCS for differentiation induction. Array data were deposited in GEO (Gene Expression Omnibus, NCBI) under accession number GSE35523. Here, we describe in detail the cell culture features and our TaqMan qPCR-experiments to validate the array-CGH analysis. Interpretation of array-CGH experiments regarding gene amplifications in mouse and further detailed analysis of amplified chromosome regions associated with these experiments were published by Fischer and colleagues in Oncotarget (Fischer et al., 2015). We provide additional information on deleted chromosome regions during differentiation and give an impressive overview on copy number changes during differentiation induction at a time line.
Department of Human Genetics, Saarland University, Building 60, 66421 Homburg/Saar, Germany.
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Fischer
Department of Human Genetics, Saarland University, Building 60, 66421 Homburg/Saar, Germany.
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Ludwig
Clinical Bioinformatics, Saarland University, Building E2.1, 66123 Saarbrücken, Germany.
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Keller
Clinical Bioinformatics, Saarland University, Building E2.1, 66123 Saarbrücken, Germany.
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Backes
Department of Human Genetics, Saarland University, Building 60, 66421 Homburg/Saar, Germany.
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Meese
Array-CGH; Gene amplification; Neural stem cell differentiation; qPCR