Mouse_Cortical_Region_snRNAseq data
Genotype Group: 5xFAD_WT, BIN1HO, 5xFAD_HEMI, 5xFAD_HEMI-BIN1HO
Garcia-Agudo, L. F., Shi, Z., Smith, I. F., Kramár, E. A., Tran, K., Kawauchi, S., Wang, S., Collins, S., Walker, A., Shi, K. X., Neumann, J., Liang, H. Y., Da Cunha, C., Milinkeviciute, G., Morabito, S., Miyoshi, E., Rezaie, N., Gomez-Arboledas, A., Arvilla, A. M., Ghaemi, D. I., … Green, K. N. (2024). BIN1K358R suppresses glial response to plaques in mouse model of Alzheimer's disease. Alzheimer's & dementia : the journal of the Alzheimer's Association, 10.1002/alz.13767. Advance online publication. https://doi.org/10.1002/alz.13767
Dr. Laura Fernandez from Green lab at UCI
Zechuan Shi @rootze from Swarup lab at UCI
Zechuan Shi @rootze created analysis documents that combine code
Programming software:
- R v4.2.2
- Python v3.10.6
Tools_Software:
- Cellranger (v7.0.0)
- CellBender (v0.2.1)
- Seurat (v4.3.0)
- UCell (v2.2.0)
- hdWGCNA (v0.2.19)
- CellChat (v1.6.1)
- ComplexHeatmap (v2.14.0)
Reference dataset:
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Mouse reference dataset required for Cell Ranger: md5sum: 886eeddde8731ffb58552d0bb81f533d (refdata-gex-mm10-2020-A)
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Celltypes label reference: Mouse brain SPLiT-seq data
Rosenberg, A. B., Roco, C. M., Muscat, R. A., Kuchina, A., Sample, P., Yao, Z., Graybuck, L. T., Peeler, D. J., Mukherjee, S., Chen, W., Pun, S. H., Sellers, D. L., Tasic, B., & Seelig, G. (2018). Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding. Science (New York, N.Y.), 360(6385), 176–182. (Paper_Link)
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Disease-associated oligodendrocytes: Male AppNL-G-F and male 5xFAD AD mouse brains
Park, H., Cho, B., Kim, H., Saito, T., Saido, T. C., Won, K. J., & Kim, J. (2023). Single-cell RNA-sequencing identifies disease-associated oligodendrocytes in male APP NL-G-F and 5XFAD mice. Nature communications, 14(1), 802. (Paper_Link)
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