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Spatial transcriptomics of fixed tissue micro-regions using Pick-Seq [melanoma]

ABSTRACT: Spatial transcriptomics of fixed tissue micro-regions using Pick-Seq [melanoma]

PROVIDER: PRJNA665648 | ENA |

REPOSITORIES: ENA

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Spatial transcriptomics of fixed tissue micro-regions using Pick-Seq

Project description:Spatial transcriptomics of fixed tissue micro-regions using Pick-Seq

| PRJNA665645 | ENA

Spatial transcriptomics of fixed tissue micro-regions using Pick-Seq [melanoma]

Project description:Spatial transcriptomics and multiplexed imaging are complementary methods for studying tissue biology. Here we describe a simple method for transcriptional profiling of formalin fixed histology specimens based on mechanical isolation of tissue micro-regions containing 5-20 cells. Sequencing micro-regions from an archival melanoma specimen having multiple distinct histologies reveals significant differences in transcriptional programs associated with tumor invasion, proliferation, and immunoediting and parallel imaging confirms changes in immuno-phenotypes and cancer cell states.

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Spatial transcriptomics of fixed tissue micro-regions using Pick-Seq [breast]

Project description:Spatial transcriptomics of fixed tissue micro-regions using Pick-Seq [breast]

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Spatial transcriptomics of fixed tissue micro-regions using Pick-Seq [tonsil]

Project description:Spatial transcriptomics of fixed tissue micro-regions using Pick-Seq [tonsil]

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Spatial transcriptomics of fixed tissue micro-regions using Pick-Seq [tonsil]

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Spatial transcriptomics of fixed tissue micro-regions using Pick-Seq [breast]

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Spatial transcriptomics of fixed tissue micro-regions using Pick-Seq

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-09-01 | GSE158564 | GEO

MASP micro-specimen samples at different spatial locations

Project description:Quantitative protein mapping on whole-tissue levels provides important insights into the spatially-organized regulatory processes/networks related to diseases and therapy, but remains a tremendous challenge. We describe a micro-scaffold assisted spatial proteomics(MASP) method, based on precise tissue spatial-compartmentalization using a 3D-printed micro-scaffold, capable of mapping thousands of proteins across a whole-tissue slice with excellent quantitative quality. The mapping accuracy was validated and applied in mapping >5,000 cerebral proteins in mouse brain. Under stringent cutoffs, 5019 unique proteins were mapped(N=208 micro-specimens) and 4577 proteins were mapped in all regions.

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Genome-wide Spatial Expression Profiling in Formalin-fixed Tissues

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Project description:Current spatial transcriptomic methods have been widely used to resolve gene expression; however, these methods are limited to fresh or fresh-frozen samples due to unsuccess of oligo(dT) primers in degraded RNA samples. Here we develop a spatial random-sequencing (spRandom-seq) technology for Formalin-fixed paraffin-embedded (FFPE) tissues by capturing full-length total RNAs with random primers. This approach provides a powerful spatial platform for clinical FFPE specimens and promises enormous applications in biomedicine.

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