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| Status |
Public on Apr 19, 2021 |
| Title |
Seq-Scope: Submicrometer-resolution spatial barcoding technology that enables microscopic examination of tissue transcriptome at single cell and subcellular levels |
| Organisms |
Mus musculus; synthetic construct |
| Experiment type |
Other
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| Summary |
Purpose: we propose Sequence-Scope (Seq-Scope), which can generate ultra-high definition images of sequence-based molecular signatures resolved at a submicrometer scale.
Experimental Methods: Seq-Scope experiment is divided into two consecutive sequencing steps: 1st-Seq and 2nd-Seq. 1st-Seq of Seq-Scope starts with the solid-phase amplification of a single-stranded synthetic oligonucleotide library using an Illumina sequencing-by-synthesis (SBS) platform. 2nd-Seq of Seq-scope begins with overlaying the tissue section slice onto the HDMI-array. Computational Methods: Tissue boundaries are detected by using a custom python code to draw a smoothed density plot to visualize the density of HiSeq reads in a given XY space of each tile. Digital gene expression (DGE) matrices are generate using STAR/STARsolo 2.7.5c with Gene,GeneFull, Velocyto, and polyAtrimming options. Data binning is performed by dividing the imaging space into 100 μm2 square grid with 10 μm simple side or 25 μm2 square grid with 5 μm side and collapsing all HDMI-UMI information into one barcode. Binned DGE matrix was analyzed in the Seurat v4 package for clustering analysis.
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| Overall design |
A total of 2 Seq-Scope experiments (colon and liver) were run. Livers were collected from 8 week-old control (Depdc5F/F/Tsc1F/F, male) and TD (Alb-Cre/Depdc5F/F/Tsc1F/F, female) mice. Colons are from 8-week-old C57BL/6 wild-type male mice.
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| Contributor(s) |
Cho C, Xi J, Si Y, Lee JH, Kang HM, Park S, Hsu J, Kim M, Jun G |
| Citation(s) |
34115981 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 DK102850 |
Mechanisms underlying Hepatoprotective Roles of Sestrin2 |
REGENTS OF THE UNIVERSITY OF MICHIGAN - ANN ARBOR |
Jun Hee Lee |
| R01 DK114131 |
Protein inclusions in non-alcoholic steatohepatitis |
REGENTS OF THE UNIVERSITY OF MICHIGAN - ANN ARBOR |
Jun Hee Lee |
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| Submission date |
Mar 26, 2021 |
| Last update date |
Jul 19, 2021 |
| Contact name |
Jun Hee Lee |
| E-mail(s) |
leeju@umich.edu
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| Organization name |
University of Michigan
|
| Street address |
109 Zina Pitcher Pl
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109-2200 |
| Country |
USA |
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| Platforms (3) |
| GPL17769 |
Illumina MiSeq (synthetic construct) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
| GPL21273 |
HiSeq X Ten (Mus musculus) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA717741 |
| SRA |
SRP312324 |
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