GSE107399
Rett Syndrome in a dish model
Several recent studies have suggested that genes that are longer than 100 kb are more likely to be misregulated in neurological diseases associated with synaptic dysfunction, such as autism and Rett syndrome. These length-dependent transcriptional changes are modest in Mecp2 mutant samples, but, given the low sensitivity of high-throughput transcriptome profiling technology, the statistical significance of these results needs to be re-evaluated. Here, we show that the apparent length-dependent trends previously observed in MeCP2 microarray and RNA-Sequencing datasets, particularly in genes with low-fold changes, disappeared when compared to randomized control samples. As we found no similar bias with Nanostring technology, this bias seems to be particular to PCR amplification-based platforms. Transcriptional alterations with large fold-change values, however, can reveal an authentic long gene bias. Discriminating authentic from artefactual length-dependent trends requires establishing a baseline from randomized control samples. Overall design: RNA-Seq iPSC, NPC and Neuron dataset of Rett Syndrome