UCSD to Use Single-Cell Sequencing to Create 3D Transcriptional Map of Brain

http://www.genomeweb.com/sequencing/ucsd-use-single-cell-sequencing-create-3d-transcriptional-map-brain?hq_e=el&hq_m=1419571&hq_l=2&hq_v=637acc240e

The project has two main components, Zhang told In Sequence. The first part involves using microdissection or flow sorting techniques to grab individual cells from brain tissue and perform RNA-seq on each of the cells. For this, the team plans to do 10,000 single-cell transcriptomes by the end of the five years.

The second part of the project involves developing an in situ RNA-seq protocol to act as a "fingerprint" for transcriptional location, so the transcriptomes of the individual cells can be placed within the context of the brain. For this part, the plan is to assemble at least 500 transcripts.

 Zhang said that they are aiming to do 10,000 cells because the human brain is so diverse. Not only are there many different cell types, but even within the same type of cell, there is a huge amount of variability. "To do a comprehensive characterization, we need to sample a large enough amount … We decided to do 10,000, because only when we get to that scale might we be able to get to an accurate picture of what's going on in the human adult brain."