How to use POSTGis with RNA-sequence (Transcriptomic) coordinates
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The tissues in our bodies are complex systems composed of diverse celltypes that often interact in highly structured repeating anatomical units. Some of the major challenges in research today include understanding disease progression and classifying diseases based on molecular markers. Obtaining quantitative information about gene-expression changes within cells in their native environment is laborious and challenging. How would you quantify the entire transcriptomes of cells while accounting for their spatial coordinates? However, methods that combine traditional histology with transcriptome data are already available or under development—some can capture the full transcriptome in a standard-size tissue section, while others focus on subsets of mRNAs with single-cell resolution. A new technology termed “spatial transcriptomics” uses spatially barcoded, complementary DNA primers for full-transcriptome capture on tissue sections, and can be applied alone or in combination with single-cell technologies.
Spatial transcriptomics is a technology used to spatially resolve RNA-seq data, and thereby all mRNAs, in individual tissue sections. I'll demonstrate how we use POSTGIS to store and retrieve rna-seq data for our in-house analysis and pipelines.
- 2019 June 20 - 12:30
- 50 min
- PostgreSQL Ibiza
- Track 2
- The Art of PostgreSQL
- Start Time:
- 2019 June 20 12:30