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| Status |
Public on May 21, 2023 |
| Title |
Spatial Multimodal Analysis: MALDI-MSI and Spatial Transcriptomics within the same tissue section |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
We present a spatial omics approach that merges and expands the capabilities of independently performedin situassays on a single tissue section. Our spatial multimodal analysis combines histology, mass spectrometry imaging, and spatial transcriptomics to facilitate precise measurements of mRNA transcripts and low-molecular weight metabolites across tissue regions. We demonstrate the potential of our method using murine and human brain samples in the context of dopamine and Parkinson’s disease.
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| Overall design |
Tissue sections processed with MALDI-MSI were eventually analyzed using Visium. Controls for some of the samples are included.
*** From Submitter: We are restricted to deposit raw sequencing from humans to SRA. Those will be deposited on the Swedish federated EGA node and we will link when it became available to us. ***
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| Contributor(s) |
Vicari M, Mirzazadeh R, Nilsson A, Shariatgorji R, Bjärterot P, Larsson L, Lee H, Nilsson M, Foyer J, Ekvall M, Czarnewski P, Zhang X, Svenningsson P, Andrén PE, Lundeberg J |
| Citation(s) |
37667091 |
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| Submission date |
May 19, 2023 |
| Last update date |
Aug 09, 2024 |
| Contact name |
Marco Vicari |
| E-mail(s) |
[email protected]
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| Organization name |
KTH, SciLifeLab
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| Department |
Gene Technology
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| Lab |
Joakim Lundeberg
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| Street address |
Tomtebodavägen 23
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| City |
Solna |
| ZIP/Postal code |
171 65 |
| Country |
Sweden |
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| Platforms (2) |
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| Samples (19)
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| GSM7392310 |
mouse brain, Striatum, 6-OHDA, mouse3, DHB (V11L12-038_A1) |
| GSM7392311 |
mouse brain, Striatum, 6-OHDA, mouse3, DHB (V11L12-038_B1) |
| GSM7392312 |
mouse brain, Striatum, 6-OHDA, mouse3, iCTRL (V11L12-038_C1) |
| GSM7392313 |
mouse brain, Striatum, 6-OHDA, mouse3, 9-AA (V11L12-038_D1) |
| GSM7392314 |
mouse brain, Striatum, 6-OHDA, mouse1, FMP-10 (V11L12-109_A1) |
| GSM7392315 |
mouse brain, Striatum, 6-OHDA, mouse3, FMP-10 (V11L12-109_B1) |
| GSM7392316 |
mouse brain, Striatum, 6-OHDA, mouse4, FMP-10 (V11L12-109_C1) |
| GSM7392317 |
mouse brain, Striatum, 6-OHDA, mouse3, FMP-10_iCTRL (V11L12-109_D1) |
| GSM7392318 |
mouse brain, Substantia Nigra, 6-OHDA, mouse1, FMP-10 (V11T16-085_A1) |
| GSM7392319 |
mouse brain, Substantia Nigra, 6-OHDA, mouse3, FMP-10 (V11T16-085_B1) |
| GSM7392320 |
mouse brain, Substantia Nigra, 6-OHDA, mouse4, FMP-10 (V11T16-085_C1) |
| GSM7392321 |
mouse brain, Substantia Nigra, 6-OHDA, mouse4, FMP-10_iCTRL (V11T16-085_D1) |
| GSM7392322 |
mouse brain, Substantia Nigra, 6-OHDA, mouse1, Visium (V11T17-101_A1) |
| GSM7392323 |
mouse brain, Striatum, 6-OHDA, mouse3, Visium (V11T17-101_B1) |
| GSM7392324 |
human post-mortem brain, Striatum, PD, Visium (V11T17-101_D1) |
| GSM7392325 |
human post-mortem brain, Striatum, PD, FMP-10 (V11T17-102_A1) |
| GSM7392326 |
human post-mortem brain, Striatum, PD, FMP-10 (V11T17-102_B1) |
| GSM7392327 |
human post-mortem brain, Striatum, PD, FMP-10 (V11T17-102_C1) |
| GSM7392328 |
human post-mortem brain, Striatum, PD, FMP-10 (V11T17-102_D1) |
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| Relations |
| BioProject |
PRJNA974409 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE232910_RAW.tar |
4.6 Gb |
(http)(custom) |
TAR (of CSV, H5, JPG, JSON, PNG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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