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Series GSE151137 Query DataSets for GSE151137
Status Public on Jun 28, 2020
Title Integrating single-cell RNA-seq and imaging with SCOPE-seq2
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Live cell imaging allows direct observation and monitoring of phenotypes that are difficult to infer from the transcriptome. 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), which builds on our earlier efforts to combine 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 demonstrated 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.
Overall design Perfromed SCOPE-seq v2 on mixed human (U87) and mouse (3T3) cells, and cells collected from human glioblastoma.
Contributor(s) Yuan J, Liu Z, Sims P
Citation(s) 33173156
Submission date May 25, 2020
Last update date Jul 27, 2022
Contact name Peter Sims
Organization name Columbia University
Street address 3960 Broadway
City New York
State/province NY
ZIP/Postal code 10032
Country USA
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19415 Illumina NextSeq 500 (Homo sapiens; Mus musculus)
Samples (2)
GSM4567139 U87_3T3_scRNAseq [PJ0707172]
GSM4567140 GBM_scRNAseq [PJ069]
BioProject PRJNA634853
SRA SRP263460

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Supplementary file Size Download File type/resource
GSE151137_RAW.tar 46.6 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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