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| Status |
Public on Sep 09, 2019 |
| Title |
High-density spatial transcriptomics arrays for in situ tissue profiling |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Tissue function relies on the precise spatial organization of cells characterized by distinct molecular profiles. Single-cell RNA-Seq captures molecular profiles but not spatial organization. Conversely, spatial profiling assays to date have lacked global transcriptome information, throughput or single-cell resolution. Here, we develop High-Density Spatial Transcriptomics (HDST), a method for RNA-Seq at high spatial resolution. Spatially barcoded reverse transcription oligonucleotides are coupled to beads that are randomly deposited into tightly packed individual microsized wells on a slide. The position of each bead is decoded with sequential hybridization using complementary oligonucleotides providing a unique bead-specific spatial address. We then capture, and spatially in situ barcode, RNA from the histological tissue sections placed on the HDST array. HDST recovers hundreds of thousands of transcript-coupled spatial barcodes per experiment at 2 μm resolution. We demonstrate HDST in the mouse brain, use it to resolve spatial expression patterns and cell types, and show how to combine it with histological stains to relate expression patterns to tissue architecture and anatomy. HDST opens the way to spatial analysis of tissues at high resolution.
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| Overall design |
Three sections of the main olfactory bulb from adult C57BL/6J mice
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| Contributor(s) |
Vickovic S, Bergenstråhle L |
| Citation(s) |
31501547 |
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| Submission date |
May 03, 2019 |
| Last update date |
Sep 20, 2019 |
| Contact name |
Sanja Vickovic |
| E-mail(s) |
vickovic@broadinstitute.org
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| Organization name |
Broad Institute
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| Street address |
415 Main Street
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| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA540976 |
| SRA |
SRP194917 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE130682_RAW.tar |
867.0 Mb |
(http)(custom) |
TAR (of TIFF, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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