 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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) |
|
| Relations |
| BioProject |
PRJNA634853 |
| SRA |
SRP263460 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE151137_RAW.tar |
46.6 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
