Transcriptome analysis of genetically matched human induced pluripotent stem cells disomic or trisomic for chromosome 21

Trisomy of chromosome 21, the genetic cause of Down syndrome, has the potential to alter expression of genes on chromosome 21, as well as other locations throughout the genome. These transcriptome changes are likely to underlie the Down syndrome clinical phenotypes. We have employed RNA-seq to undertake an in-depth analysis of transcriptome changes resulting from trisomy of chromosome 21, using induced pluripotent stem cells (iPSCs) derived from a single individual with Down syndrome. These cells were originally derived by Li et al, who genetically targeted chromosome 21 in trisomic iPSCs, allowing selection of disomic sibling iPSC clones. Analyses were conducted on trisomic/disomic cell pairs maintained as iPSCs or differentiated into cortical neuronal cultures. Overall design: 12 total polyA selected samples. 6 IPSC samples with 3 biological repeats for trisomic samples and 3 biological repeats for disomic samples. 6 IPSC derived neuronal samples with 3 biological repeats for trisomic samples and 3 biological repeats for disomic samples.