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Integrating single-cell RNA-seq and imaging with SCOPE-seq2.


ABSTRACT: Live cell imaging allows direct observation and monitoring of phenotypes that are difficult to infer from transcriptomics. However, existing methods for linking microscopy and single-cell RNA-seq (scRNA-seq) have limited scalability. Here, we describe an upgraded version of Single Cell Optical Phenotyping and Expression (SCOPE-seq2) for combining single-cell imaging and expression profiling, with substantial improvements in throughput, molecular capture efficiency, linking accuracy, and compatibility with standard microscopy instrumentation. We introduce improved optically decodable mRNA capture beads and implement a more scalable and simplified optical decoding process. We demonstrate the utility of SCOPE-seq2 for fluorescence, morphological, and expression profiling of individual primary cells from a human glioblastoma (GBM) surgical sample, revealing relationships between simple imaging features and cellular identity, particularly among malignantly transformed tumor cells.

SUBMITTER: Liu Z 

PROVIDER: S-EPMC7655825 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Integrating single-cell RNA-seq and imaging with SCOPE-seq2.

Liu Zhouzerui Z   Yuan Jinzhou J   Lasorella Anna A   Iavarone Antonio A   Bruce Jeffrey N JN   Canoll Peter P   Sims Peter A PA  

Scientific reports 20201110 1


Live cell imaging allows direct observation and monitoring of phenotypes that are difficult to infer from transcriptomics. However, existing methods for linking microscopy and single-cell RNA-seq (scRNA-seq) have limited scalability. Here, we describe an upgraded version of Single Cell Optical Phenotyping and Expression (SCOPE-seq2) for combining single-cell imaging and expression profiling, with substantial improvements in throughput, molecular capture efficiency, linking accuracy, and compatib  ...[more]

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