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Spatial Genomics: in situ transcriptome profiling by RNA seqFISH+

CMCB Life Sciences Seminar

Datum:04/06/2020, 17:00 - 18:00
Sprecher: Long Cai, California Institute of Technology
Ort: Zoom Video Conferencing
Gastgeber: Nikolay Ninov

Link to the conference -  Meeting ID: 961 6566 0841, Password: 0X=V&s

Abstract:

Imaging the transcriptome in situ with high accuracy has been a major challenge in single cell biology, particularly hindered by the limits of optical resolution and the density of transcripts in single cells. We developed seqFISH+, that can image the mRNAs for 10,000 genes in single cells with high accuracy and sub-diffraction-limit resolution, in the mouse brain cortex, subventricular zone, and the olfactory bulb, using a standard confocal microscope. The transcriptome level profiling of seqFISH+ allows unbiased identification of cell classes and their spatial organization in tissues. In addition, seqFISH+ reveals subcellular mRNA localization patterns in cells and ligand-receptor pairs across neighboring cells. This technology demonstrates the ability to generate spatial cell atlases and to perform discovery-driven studies of biological processes in situ.

5 most important publications:

1. Eng, Chee-Huat Linus, Michael Lawson, Qian Zhu, Ruben Dries, GC Yuan, and Long Cai. “Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+"  Nature. 2019 (7751):235-239. 
2. Sheel Shah, Yodai Takei, Wen Zhou, Eric Lubeck, Jina Yun, Mina Amin, Long Cai.  Dynamics of global transcriptional activity in single stem cells by intron seqFISH.  Cell.  2018.  174, 1-14, July 12, 2018.  Published online June 7, 2018. 
3. 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. 2017. 541(7635):107-111. doi: 10.1038/nature20777.
4. Sheel Shah, Eric Lubeck, Wen Zhou, and Long Cai.  In situ transcription profiling of single cells in brain slices reveals spatial organization of the hippocampus.  Neuron. 2016. 92: 342-357. 
5. 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