Expression of 97 surface markers and RNA (transcriptome wide) in 13165 cells from a healthy young bone marrow donor

Seurat v3 object

ASSAYS:

AB: Antibody expression data

RNA: mRNA expression data

BOTH: Concatenated mRNA and antbody expression matrices

DIMENSIONALITY REDUCTION

MOFA: Multi-OMICS factor analysis to integrate AB and RNA data. MOFA served as input for clustering and further dimensionality reduction.

MOFAUMAP: UMAP performed on MOFA dimensions. Display used in the manuscript.

MOFATSNE: UMAP performed on MOFA dimensions.

Projected: Data was projected on the reference dataset MOFAUMAP coordinates

METADATA

ct: Projected cell type (cell type labels from the reference dataset are used).

Idents(object) uses an unsupervised clustering performed on this dataset.

For the reference dataset, see https://doi.org/10.6084/m9.figshare.13397651.v2

Changelog

v3: Compared to the previous version of the file, projected UMAP coordinates and projected cell type labels were added. Also, neighborhood graphs and normalized data are now contained in the object.

v4: Objects were slimed to correspond to the information described in our study. Data now only contains relevant dimensions reductions and metadata columns; unused RNA and antibody targets were excluded from the objects.