Lee, Je H. (July 2017) De Novo Gene Expression Reconstruction in Space. Trends in Molecular Medicine, 23 (7). pp. 583-593. ISSN 1471-4914
Abstract
The biological function of a gene often depends on spatial context, and an atlas of transcriptional regulation could be instrumental in defining functional elements across the genome. Despite recent advances in single-cell RNA sequencing and in situ RNA imaging, fundamental barriers limit the speed, genome-wide coverage, and resolution of de novo transcriptome assembly in space. Here, I discuss potential next-generation approaches for the de novo assembly of the transcriptome in space, and propose more efficient methods of detecting long-range spatial variations in gene expression. Finally, I discuss future in situ sequencing chemistries for visualizing biological pathways and processes in tissues so that genomics technologies might be more easily applied to conditions of human health and disease.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | gene expression atlas single cell RNA sequencing multiplex single-molecule FISH in situ sequencing FISSEQ |
| Subjects: | bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression Investigative techniques and equipment > assays > RNA-seq |
| CSHL Authors: | |
| Communities: | CSHL Cancer Center Program > Cancer Genetics CSHL labs > Lee lab Northwell Health CSHL Cancer Center Program > Cancer Genetics and Genomics Program |
| Depositing User: | Matt Covey |
| Date: | July 2017 |
| Date Deposited: | 05 Jun 2017 20:31 |
| Last Modified: | 05 Nov 2020 21:34 |
| PMCID: | PMC5514424 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/34812 |
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