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| Status |
Public on Dec 05, 2021 |
| Title |
10X Visium Spatial transcriptomics of murine colon in steady state and during recovery after DSS colitis |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The limitation of single-cell or bulk transcriptomic profiling is the lack of spatial topographical context. Spatial transcriptomics (ST) allows sequencing of polyadenylated transcripts from a tissue section which can be spatially mapped onto the histological brightfield image using an array of barcoded oligo-dT capturing probes. Using the 10X Visium platform, here, we unbiasedly characterized the spatial transcriptomic landscape of murine colon in steady state and during mucosal healing upon dextran sodium sulfate (DSS) induced injury
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| Overall design |
Wild type C57BL/6J mice were exposed to DSS in drinking water for 7 days and then allowed to recover for 7 more days. Mouse colonic tissues were collected either on day 0 (without any exposure to DSS) or on day14 after exposure to DSS, Swisrolled and frozen in OCT. Mouse colonic tissues (day0 and day14) were cryo-sectioned (10uM) and placed on the already barcoded spots (6.5mm x 6.5mm) on the glass slide. Samples were processed according to 10X Visium spatial transcriptomics protocol and submitted for sequencing.
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| Contributor(s) |
Das S, Villablanca E, Larsson L |
| Citation(s) |
35149721 |
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| Submission date |
Mar 26, 2021 |
| Last update date |
Mar 06, 2022 |
| Contact name |
Ludvig Ale Larsson |
| E-mail(s) |
ludvig.larsson@scilifelab.se
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| Phone |
+46739911122
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| Organization name |
SciLifeLab
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| Department |
Gene Technology
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| Street address |
Tomtebodavägen 23A
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| City |
Solna |
| State/province |
Stockholm |
| ZIP/Postal code |
17165 |
| Country |
Sweden |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA717789 |
| SRA |
SRP312361 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE169749_RAW.tar |
807.8 Mb |
(http)(custom) |
TAR (of CSV, H5, JSON, PNG, TIFF, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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