mTopic - Supplementary RDS data

Uploaded files are raw (*_raw.rds) and filtered (*_filtered.rds) RDS objects used for R tutorials of mTopic.

Single-cell data processed here are publicly available from the Gene Expression Omnibus (GEO) and 10x Genomics:

P22 mouse brain dataset (P22_Mouse_Brain_ATAC_RNA) [1]

– GSE218593 (GSM6753043) for RNA
– GSE205055 (GSM6758285) for ATAC

Human tonsil dataset (Human_Tonsil_RNA_Protein)

Available from 10x Genomics here.

Human PBMC dataset (Human_PBMC_ATAC_RNA_Protein) [2]

GSE166188
– GSM5065524 for ATAC
– GSM5065525 for RNA
– GSM5065526 for protein

References

[1] Zhang D, Deng Y, Kukanja P, Agirre E et al. Spatial epigenome-transcriptome co-profiling of mammalian tissues. Nature 2023 Apr;616(7955):113-122. PMID: 36922587
[2] Mimitou EP, Lareau CA, Chen KY, Zorzetto-Fernandes AL et al. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells. Nat Biotechnol 2021 Oct;39(10):1246-1258. PMID: 34083792