ENCODE4 Mouse snRNA-seq and snATAC-seq Analysis

Cell type annotation overview

Postnatal timecourse of B6/Cast F1 hybrid mouse development in 5 core tissues: cortex, hippocampus, heart, adrenal gland, and gastrocnemius, at 7 timepoints for Parse snRNA-seq: PND04, PND10, PND14, PND25, PND36, PNM02, and PNM18-20 and 2 timepoints for 10x Multiome snRNA-seq+snATAC-seq: PND14 and PNM02, with 2 males and 2 females per timepoint.

Parse snRNA Demultiplexing

Run split-pipe per sublibrary and demultiplex fastqs for each sample (individual mouse) for submissoion to the ENCODE portal:

Integrated snRNA analysis

Download snRNA-seq counts matrices from the ENCODE portal, filter genes, detect ambient RNA (Cellbender), and detect doublets (Scrublet):

B6CAST Adrenal, 10x data cart and Parse data cart
B6CAST Cortex, 10x data cart and Parse data cart
B6CAST Hippocampus, 10x data cart and Parse data cart
B6CAST Heart, 10x data cart and Parse data cart
B6CAST Gastrocnemius, 10x data cart and Parse data cart
B6CAST/5xFAD cortex/hippocampus Parse data cart
B6/5xFAD cortex/hippocampus GEO link and ENCODE link to processed data

Integrated Seurat processing and cell type annotation. If the data includes 10x Multiome, snATAC preprocessing code must be run first! 10x Multiome nuclei are filtered by both RNA and ATAC quality metrics. Annotation of Seurat clusters is performed within Jupyter notebooks.

B6CAST Adrenal, annotation notebook
B6CAST Cortex, annotation notebook
B6CAST Hippocampus, annotation notebook
B6CAST Heart, annotation notebook
B6CAST Gastrocnemius, annotation notebook
B6CAST/5xFAD cortex/hippocampus
B6/5xFAD cortex/hippocampus

snATAC analysis

Download fragments files from ENCODE snATAC standard pipeline, construct ArchR projects, and filter nuclei by > 1,000 fragments, > 4 TSS enrichment, and remove doublets: