Description

Single Cell Expression Profiling and Lineage Dynamics by seqFISH and MEMOIR

Long Cai

California Institute of Technology, Pasadena, CA, USA

Identifying the spatial organization of tissues at cellular resolution from single cellgene expression profiles is essential to understanding many biological systems. We have developed an in situ 3D multiplexed imaging method to quantify hundreds of genes with single cell resolution via Sequential barcodedFluorescence in situ hybridization (seqFISH) (Lubeck et al., 2014). We used seqFISH to identifyunique transcriptional states by quantifying and clustering up to 249 genes in 16,958 cells. By visualizing these clustered cells in situ, we identified regions within distinct composition of cells in different transcriptional states. Together, these resultsdemonstrate the power of seqFISH in transcriptional profiling of complex tissues.Lastly, I will discuss our work in writing lineages and cell event history into genome of cells by CRISPR/Cas9 genome editing and reading out the stored information in single cells by seqFISH.

Reference:

Lubeck E, Coskun AF, Zhiyentayev T, Ahmad M, Long Cai. Single-cell in situ RNA profiling by sequential hybridization. Nat Methods. 2014 Apr;11(4):360-1. PMCID: PMC4085791.

Shah, Lubeck, Zhou and Cai, In situ transcription profiling of single cells reveals spatial organization of cells in the mouse hippocampus.Neuron (2016) Oct 19th. https://dx.doi.org/10.1016/j.neuron.2016.10.001

Kirsten L. Frieda, James M. Linton, Sahand Hormoz, Joonhyuk Choi, Ke-Huan K. Chow, Zakary S. Singer, Mark W. Budde, Michael B. Elowitz*, Long Cai*. Synthetic recording and in situ readout of lineage information in single cells.Nature. 2016.Published online Nov 21st.