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

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. Columbia University researchers 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. The researchers introduce improved optically decodable mRNA capture beads and implement a more scalable and simplified optical decoding process. They 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.

Overview of SCOPE-seq2

(A) A schematic representation of the experimental workflow for SCOPE-seq2. (B) Oligonucleotide design for SCOPE-seq2 optically decodable mRNA capture beads. (C) Split-pool synthesis scheme for generating combinatorial SCOPE-seq2 barcodes with the structure shown in (B). (D) Schematic for generating pools of fluorescent probes for SCOPE-seq2 optical decoding.