Title: Integrative in situ mapping of single-cell transcriptional states and tissue histopathology in a mouse model of Alzheimers disease
Authors: Hu Zeng, Jiahao Huang, Haowen Zhou, William J Meilandt, Borislav Dejanovic, Yiming Zhou, Christopher J Bohlen, Seung-Hye Lee, Jingyi Ren, Albert Liu, Zefang Tang, Hao Sheng, Jia Liu, Morgan Sheng, Xiao Wang
Date published: 2/2/23
Date added: 12/1/23
Journal: Nature Neuroscience
DOI: 10.1038/s41593-022-01251-x
Protocol: STARmap PLUS
Data source: SCP1375
Species: mouse
Number of samples: 12
Region: Hippocampus, cerebellum
Figure: Simultaneous mapping of cell types, single-cell transcriptional states and tissue histopathology by STARmap PLUS.
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ssREAD sample ID: ST01701
Sample raw name: ADmouse_11346
Total spots in the plot: 582
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Gene expression
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Note: The MAST package were used to calculate DEGs on normalized gene expression data (parameter: log2FC > 0.25, adj.p-value < 0.05).
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| Gene name | Log fold-change | Pct.1 | Pct.2 | Adjusted p-value |
|---|---|---|---|---|
| S100a8 | 6.26858 | 1 | 0.085 | 6.39e-71 |
| S100a9 | 6.02366 | 0.958 | 0.044 | 7.78e-52 |
| Msrb1 | 3.56581 | 0.958 | 0.14 | 4.88e-41 |
| Wfdc17 | 3.88857 | 0.958 | 0.195 | 7.58e-39 |
| Il1b | 3.51356 | 0.958 | 0.177 | 3.70e-38 |
| S100a11 | 3.40736 | 1 | 0.094 | 1.59e-32 |
| Ifitm1 | 3.92665 | 0.875 | 0.034 | 1.21e-31 |
| Wfdc21 | 3.63095 | 0.75 | 0.007 | 6.01e-30 |
| Slpi | 3.52733 | 0.792 | 0.011 | 2.44e-28 |
| Hp | 2.422 | 0.75 | 0.013 | 4.77e-24 |
| Retnlg | 4.83923 | 0.583 | AGPAT5 | 1.00e-22 |
| Lrg1 | 2.47749 | 0.625 | 0.004 | 3.60e-22 |
| Il1f9 | 2.45794 | 0.583 | 0.002 | 6.03e-22 |
| S100a6 | 2.92084 | 0.833 | 0.076 | 1.26e-19 |
| Hdc | 2.35431 | 0.583 | 0.012 | 2.34e-18 |