AD brain analysis

Data analysis pipeline by Kun Leng, Kampmann lab, 2020.

Download the zipped directory here (74 GB).

This directory contains the full analysis of the single-nucleus RNA-sequencing (snRNA-seq) data in Leng, Li et al. (2020) and reproduces all figures pertaining to the snRNA-seq data in the manuscript. The R code used for the analysis can be found in R Markdown notebooks in the folder "R". Intermediate data objects generated during the analysis can be found in the folder "processedData", and any plots and tables generated during the analysis are located in the folder "figures". Any data from external sources used in the analysis can be found in the folder "externalData".
The raw data used for the analysis (UMI count matrices from CellRanger) can be downloaded here:
UMI count matrices are available under the "Supplementary file" section on GEO.

R data objects of post-QC single cell data can be found on Synapse:!Synapse:syn21788402/wiki/601825



Kun Leng, Emmy Li, Rana Eser, Antonia Piergies, Rene Sit, Michelle Tan, Norma Neff, Song Hua Li, Roberta Diehl Rodriguez, Claudia Kimie Suemoto, Renata Elaine Paraizo Leite, Carlos A. Pasqualucci, William W. Seeley, Salvatore Spina, Helmut Heinsen, Lea T. Grinberg, Martin Kampmann
Nature Neuroscience 2021 Feb;24(2):276-287.