mTopic - Supplementary h5mu data

This record contains processed multimodal datasets stored as MuData .h5mu objects. The files were generated for analysis with mTopic.

For each dataset, three files are provided:

• *_raw.h5mu: MuData object before filtering and model training.
• *_filtered.h5mu: MuData object after filtering performed with mTopic.
• *_trained.h5mu: filtered MuData object after training with mTopic.

All datasets processed here are publicly available from the Gene Expression Omnibus (GEO) and 10x Genomics.

P22 mouse brain datasets

Files:

• P22MouseBrainATAC_*
• P22MouseBrainH3K4me3_*
• P22MouseBrainH3K27ac_*
• P22MouseBrainH3K27me3_*

These datasets are from Zhang et al. [1].

RNA data were obtained from GSE218593
– GSM6753043: ATAC-RNA
– GSM6753046: H3K4me3-RNA
– GSM6753045: H3K27ac-RNA 
– GSM6753044: H3K27me3-RNA

ATAC and histone-modification data were obtained from GSE205055 
– GSM6758285: ATAC-RNA
– GSM6704980: H3K4me3-RNA
– GSM6704978: H3K27me3-RNA
– GSM6704979: H3K27ac-RNA

Human tonsil dataset

Files:

• HumanTonsil_*

The human tonsil RNA-protein dataset was obtained from 10x Genomics.

Human PBMC dataset

Files:

• HumanPBMC*

The human PBMC ATAC-RNA-protein dataset was obtained from GSE166188  and is associated with Mimitou et al. [2]:

– GSM5065524: ATAC
– GSM5065525: RNA
– GSM5065526: protein

References

[1] Zhang D, Deng Y, Kukanja P, Agirre E, et al. Spatial epigenome-transcriptome co-profiling of mammalian tissues. Nature. 2023;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. Nature Biotechnology. 2021;39(10):1246–1258. PMID: 34083792.