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| Status |
Public on Jan 13, 2020 |
| Title |
Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Single-cell RNA sequencing (scRNA-seq) enables the systematic identification of cell populations in a tissue, but characterizing their spatial organization remains challenging. We combine a microarray-based spatial transcriptomics method that reveals spatial patterns of gene expression using an array of spots, each capturing the transcriptomes of multiple adjacent cells, with scRNA-Seq generated from the same sample. To annotate the precise cellular composition of distinct tissue regions, we introduce a method for multimodal intersection analysis. Applying multimodal intersection analysis to primary pancreatic tumors, we find that subpopulations of ductal cells, macrophages, dendritic cells and cancer cells have spatially restricted enrichments, as well as distinct coenrichments with other cell types. Furthermore, we identify colocalization of inflammatory fibroblasts and cancer cells expressing a stress-response gene module. Our approach for mapping the architecture of scRNA-seq-defined subpopulations can be applied to reveal the interactions inherent to complex tissues.
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| |
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| Overall design |
Single-cell RNA-sequencing and spatial transcriptomics of primary pancreatic cancer tissue from six patients.
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| |
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| Contributor(s) |
Moncada R |
| Citation(s) |
31932730 |
| |
| Submission date |
Mar 12, 2018 |
| Last update date |
Nov 05, 2020 |
| Contact name |
Itai Yanai |
| E-mail(s) |
itai.yanai@nyumc.org
|
| Organization name |
Institute for Computational Medicine, NYU Langone Health
|
| Street address |
435 E. 30th Street, 8th Floor
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (23)
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|
| Relations |
| BioProject |
PRJNA437847 |
| SRA |
SRP134863 |
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