Single-Cell RNA-Seq Analysis of Amyloid-Induced Neurodegeneration
Amyloid toxicity was induced as described [13 (link), 47 ] in the adult telencephalon; the brains were dissected and single-cell suspensions were generated as previously described [23 (link), 24 (link)]. Chromium Single-Cell 3’ Gel Bead and Library Kit v3.1 (10X Genomics, 120,237) was used to generate single-cell cDNA libraries. Generated libraries were sequenced via Illumina NovaSeq 6000 as described [12 (link), 13 (link), 23 (link), 24 (link), 71 (link)]. The cell clusters were identified using a resolution of 1. In total, 34 clusters were identified. The main cell types were identified by using s100b and gfap for astroglia; sv2a, nrgna, grin1a, grin1b for neurons; pdgfrb and kcne4 for pericytes; cd74a and apoc1 for microglia; mbpa and mpz for oligodendrocytes; myh11a and tagln2 for vascular smooth muscle cells, kdrl for endothelial cells.
Bhattarai P., Gunasekaran T.I., Belloy M.E., Reyes-Dumeyer D., Jülich D., Tayran H., Yilmaz E., Flaherty D., Turgutalp B., Sukumar G., Alba C., McGrath E.M., Hupalo D.N., Bacikova D., Le Guen Y., Lantigua R., Medrano M., Rivera D., Recio P., Nuriel T., Ertekin-Taner N., Teich A.F., Dickson D.W., Holley S., Greicius M., Dalgard C.L., Zody M., Mayeux R., Kizil C, & Vardarajan B.N. (2024). Rare genetic variation in fibronectin 1 (FN1) protects against APOEε4 in Alzheimer’s disease. Acta Neuropathologica, 147(1), 70.
Other organizations :
Columbia University Irving Medical Center, Stanford University, Yale University, Columbia University, Henry M. Jackson Foundation, Pontificia Universidad Católica Madre y Maestra, Instituto Tecnológico de Santo Domingo, Mayo Clinic in Florida, Uniformed Services University of the Health Sciences, New York Genome Center
Chromium Single-Cell 3' Gel Bead and Library Kit v3.1 (10X Genomics, 120,237) for single-cell cDNA library generation
Illumina NovaSeq 6000 sequencing method
controls
No positive or negative controls were explicitly mentioned.
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