Jun 04, 2020; Course of talks
CMCB Life Sciences Seminar: Spatial Genomics: in situ transcriptome profiling by RNA seqFISH+
Host: Nikolay Ninov (CRTD)
TU Dresden
Fetscherstraße 105
01307 Dresden
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