Expression profiling by high throughput sequencing
Understanding neurological diseases requires tractable genetic systems. Three-dimensional (3D) neural tissue systems are an attractive choice, but it is not well understood how the transcriptome profile of these tissues is affected by encapsulating materials. Here we characterize the effect of different culturing conditions on the transcriptomic profile of induced neuronal cells and develop a method for rapid generation of 3D co-cultures of neuronal and astrocytic cells from hESCs. We perform transcriptome analysis of cells resulting from astrocytic cell differentiation. Using single-cell sequencing, we find that our system recapitulates transcriptional patterns of cell types in the human brain.
Halil Tekin, Sean Simmons, Beryl Cummings, Linyi Gao, Xian Adiconis, Cynthia C. Hession, Ayan Ghoshal, Danielle Dionne, Sourav R. Choudhury, Volkan Yesilyurt, Neville E. Sanjana, Xi Shi, Congyi Lu, Matthias Heidenreich, Jen Q. Pan, Joshua Z. Levin and Feng Zhang. Effects of 3D culturing conditions on the transcriptomic profile of stem-cell-derived neurons. Nature Biomedical Engineering 2018;2:540-554. doi: 10.1038/s41551-018-0219-9