Description

These tracks contain signal data from single-cell ATAC-seq performed on primary brain samples as described in Corces et al, 2020.

Tracks in this hub:

• Peaks - final merged peak set derived from all scATAC–seq data.
• Broad-Celltypes - one wiggle track per broad celltype (e.g. OPCs)
• Clusters - one wiggle track per identified cluster (e.g. Cluster2)
• Neuronal-Celltypes - one wiggle track per neuronal celltype (e.g. VIP Interneurons)
• Neuronal-Clusters - one wiggle track per neuronal cluster (e.g. NeuronCluster15)

Display Conventions and Configuration

Cluster colors:

•    - Cluster1 - Excitatory Neurons
•    - Cluster2 - Inhibitory Neurons
•    - Cluster3 - Excitatory Neurons
•    - Cluster4 - Excitatory Neurons
•    - Cluster5 - Other Neurons
•    - Cluster6 - Other Neurons
•    - Cluster7 - Unknown Neurons
•    - Cluster8 - OPCs
•    - Cluster9 - OPCs
•    - Cluster10 - OPCs
•    - Cluster11 - Inhibitory Neurons
•    - Cluster12 - Inhibitory Neurons
•    - Cluster13 - Astrocytes
•    - Cluster14 - Astrocytes
•    - Cluster15 - Astrocytes
•    - Cluster16 - Astrocytes
•    - Cluster17 - Astrocytes
•    - Cluster18 - Possible Doublets
•    - Cluster19 - Oligodendrocytes
•    - Cluster20 - Oligodendrocytes
•    - Cluster21 - Oligodendrocytes
•    - Cluster22 - Oligodendrocytes
•    - Cluster23 - Oligodendrocytes
•    - Cluster24 - Microglia

Broad Cell Type colors:

•    - Astrocytes
•    - ExcitatoryNeurons
•    - InhibitoryNeurons
•    - Microglia
•    - NigralNeurons
•    - Oligodendrocytes
•    - OPCs

Neuronal Cluster colors:

•    - NeuronCluster1
•    - NeuronCluster2
•    - NeuronCluster3
•    - NeuronCluster4
•    - NeuronCluster5
•    - NeuronCluster6
•    - NeuronCluster7
•    - NeuronCluster8
•    - NeuronCluster9
•    - NeuronCluster10
•    - NeuronCluster11
•    - NeuronCluster12
•    - NeuronCluster13
•    - NeuronCluster14
•    - NeuronCluster15
•    - NeuronCluster16
•    - NeuronCluster17
•    - NeuronCluster18
•    - NeuronCluster19
•    - NeuronCluster20
•    - NeuronCluster21
•    - NeuronCluster22
•    - NeuronCluster23
•    - NeuronCluster24
•    - NeuronCluster25
•    - NeuronCluster26
•    - NeuronCluster27
•    - NeuronCluster28
•    - NeuronCluster29
•    - NeuronCluster30

Neuronal Cell Type colors:

•    - BDNFneg_ExcitatoryNeurons
•    - BDNFpos_ExcitatoryNeurons
•    - vGLUT2neg_ExcitatoryNeurons
•    - LAMP5_Interneurons
•    - Parvalbumin_Interneurons
•    - Somatostatin_Interneurons
•    - Striatal_Interneurons
•    - VIP_Interneurons
•    - Striatonigral_MediumSpinyNeurons
•    - Striatopallidal_MediumSpinyNeurons

Methods

For a full or a description of the methods used, refer to Corces et al.

Dimensionality Reduction and Clustering

scATAC-seq data was clustered using iterative LSI clustering in ArchR. Seurat was then used to find clusters within the LSI dimensions. UMAP plots were also generated through Seurat.

Credits

For requests regarding the data contact ryan.corces@gladstone.ucsf.edu

References

Corces MR, Shcherbina A, Kundu S, Gloudemans MJ, Frésard L, Granja JM, Louie BH, Eulalio T, Shams S, Bagdatli ST et al. Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases. Nat Genet. 2020 Nov;52(11):1158-1168. PMID: 33106633; PMC: PMC7606627