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Series GSE55475 Query DataSets for GSE55475
Status Public on Mar 01, 2014
Title Detailed analysis of the genetic and epigenetic signature of iPS cell-derived mesodiencephalic dopaminergic neurons
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Induced pluripotent stem cells (iPSCs) harbor great promise for in vitro generation of disease-relevant cell types, such as mesodiencephalic dopaminergic (mdDA) neurons involved in Parkinson’s disease. Although iPSC-derived midbrain DA neurons have been generated, detailed genetic and epigenetic characterization of such neurons is still lacking. The goal of this study is to examine the authenticity of iPSC-derived DA neurons obtained by established protocols. We FACS-purified mdDA (Pitx3gfp/+) neurons derived from mouse iPSCs and primary mdDA (Pitx3gfp/+) neurons to analyze and compare their genetic and epigenetic features. Although iPSC-derived DA neurons largely adopt characteristics of their in-vivo counterparts, relevant deviations in global gene expression and DNA methylation were found. Hypermethylated genes, mainly involved in neurodevelopment and basic neuronal functions, consequently showed reduced expression levels. Such abnormalities should be addressed as they might affect unambiguous long-term functionality and hamper the potential of iPSC-derived DA neurons for in-vitro disease modeling or cell-based therapy.
Overall design RRBS methylation maps were generated for iPSCs cells, dopaminergic neurons derived from iPSCs and primary mesodiencephalic dopaminergic neurons
Contributor(s) Roessler R, Smallwood SA, Veenvliet JV, Pechlivanoglou P, Peng S, Chakrabarty K, Groot-Koerkamp MA, Pasterkamp RJ, Wesseling E, Kelsey G, Boddeke E, Smidt MP, Copray S
Citation(s) 24749075
Submission date Feb 28, 2014
Last update date May 15, 2019
Contact name Felix Krueger
Organization name Altos Labs
Department Bioinformatics
Street address Granta Park
City Cambridge
ZIP/Postal code CB21 6GP
Country United Kingdom
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (4)
GSM1337539 Nestin.fastq.gz
GSM1337540 IPSC_derived.fastq.gz
GSM1337541 Primary_neurons.fastq.gz
BioProject PRJNA239709
SRA SRP039084

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Supplementary file Size Download File type/resource
GSE55475_RAW.tar 53.0 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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