Code and data from Meijer and Agirre et al. 2022 "Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility."
https://doi.org/10.1101/2020.07.21.213876
pseudo bulk scATAC-seq signal for each celltype. MS associated SNPs coordenates. Peak to gene interactions predicted from scATAC and scRNA signal.
scATAC-seq Sox10-GFP+/DAPI- : https://castelobranco.shinyapps.io/SCATAC10X_2020/
sc multiome (RNA+ATAC) EAE_disease_peak and Ctrl Sox10-GFP+/DAPI- : https://castelobranco.shinyapps.io/eae_multi_act/ Gene activities fron scATAC-seq , https://castelobranco.shinyapps.io/eae_multi_rna/ Gene expression from scRNA-seq ,
sc multiome (RNA+ATAC) from 2 Gray matter control post-morten samples : https://castelobranco.shinyapps.io/hs_ctr_multi_act Gene activities fron scATAC-seq , https://castelobranco.shinyapps.io/hs_ctr_multi_rna Gene expression from scRNA-seq ,
Link to the datasets through UCSC CELL browser (thanks to Matthew L. Speir , genome.UCSC.edu): http://cells.ucsc.edu/?ds=olg-eae-ms
UCSC track hubs (thanks to Matthew L. Speir , genome.UCSC.edu):
Human: https://genome.ucsc.edu/s/mspeir/hg38_pdgfra
Mouse: https://genome.ucsc.edu/s/mspeir/mm10_pdgfra (includes both scMultiomics and scATAC-seq tracks)
GEO accession super series GSE166179 Includes:
- 10X scATAC-seq
- Bulk CutandRun
- Bulk RNA-seq
- HiChIP
- 10X single cell multiomics (ATAC+RNA)
- Plate based single cell ATAC-seq
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE166179
Human raw FastQ and CellRanger arc v.2.0.0 BAM files can be accessed through https://ega-archive.org/ :
EGAS00001005911