Human PFC snATAC-seq and snRNA-seq data
Disease Group: Alzheimer's disease vs Control; Pick’s disease vs Control
Shi, Z., Das, S., Morabito, S., Miyoshi, E., Stocksdale, J., Emerson, N., Srinivasan, S. S., Shahin, A., Rahimzadeh, N., Cao, Z., Silva, J., Castaneda, A. A., Head, E., Thompson, L., & Swarup, V. (2024). Single-nucleus multi-omics identifies shared and distinct pathways in Pick's and Alzheimer's disease. bioRxiv : the preprint server for biology, 2024.09.06.611761. https://doi.org/10.1101/2024.09.06.611761
scROAD - Single-cell Regulatory Occupancy Archive in Dementia
Website: http://swaruplab.bio.uci.edu/scROAD
All raw and processed single-nucleus ATAC, single-nucleus RNA and bulk RNA sequencing data have been deposited into the National Center for Biotechnology Information Gene Expression Omnibus (GEO) database and will be made publicly available upon publication. All data in this manuscript have been deposited in the NIH GEO database (GSE259298).
Zechuan Shi @rootze from Swarup lab at UCI
Sudeshna Das from Swarup lab at UCI
Samuel Morabito @smorabit from Swarup lab at UCI
Emily Miyoshi from Swarup lab at UCI
Zechuan Shi @rootze created analysis documents that combine code
Programming software:
- R v4.1.1 and above
- Python v3.6 and above
Tools_Software:
- Cellranger-atac (v2.0.0)
- Split-pipe (v1.0.3)
- ArchR (v1.0.2)
- Signac (v1.9.0)
- ArchRtoSignac (v1.0.4)
- Seurat (v4.3.0)
- PLINK (v1.9 & v2)
- TOBIAS (v0.14.0)
- CellBender (v0.2.1)
- Scrublet (v0.2.3)
snATAC-seq processing
Cis-regulatory Analysis and TF-regulatory network
snRNA-seq processing
GWAS summary statistics processing
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