seurat v3 object
ASSAYS:AB: Antibody expression dataRNA: mRNA expression dataBOTH: Antibody and mRNA expression matrices concatenated
DIMENSIONALITY REDUCTIONProjected: Data was projected on the reference dataset MOFAUMAP coordinates.
METADATABatch: Sample1 (Bone marrow) or Sample2 (Blood)
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
Changelogv2: Compared to the previous version of the file, projected UMAP coordinates and projected cell type labels were added.
v3: Objects were slimmed 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.v4: Added Batch information back in which was dropped from v2 to v3

seurat v3 object
ASSAYS:AB: Antibody expression dataRNA: mRNA expression dataBOTH: Antibody and mRNA expression matrices concatenated
DIMENSIONALITY REDUCTIONProjected: Data was projected on the reference dataset MOFAUMAP coordinates.
METADATABatch: Sample1 (Bone marrow) or Sample2 (Blood)
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
Changelogv2: Compared to the previous version of the file, projected UMAP coordinates and projected cell type labels were added.
v3: Objects were slimmed 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.v4: Added Batch information back in which was dropped from v2 to v3

Seurat v3 object
ASSAYS: AB: Antibody expression data RNA: mRNA expression data integrated: Antibody and mRNA expression matrices were concatenated and data was integrated across patients using scanorama
DIMENSIONALITY REDUCTION MOFA: Multi-OMICS factor analysis to integrate AB and RNA data. MOFA was run on scanorama-integrated data and served as input for clustering and further dimensionality reduction. MOFAUMAP: UMAP performed on MOFA dimensions. Projected: Cell projected into the MOFAUMAP space of a healthy dataset. Display used in the manuscript.

METADATA ct: Cell type Batch: Source individual (AML1-3, AML Q1-Q6, APL Q1-Q6)
Patient Identifier age gender Genotype AML Q1 AML116 71 f FLT3-ITD,NPM1-mut AML Q2 AML327 62 f FLT3-wt,NPM1-mut AML Q3 AML127 56 f FLT3-wt,NPM1-mut AML Q4 AML314 51 m FLT3-ITD,NPM1-mut AML Q5 AML334 78 m FLT3-wt,NPM1-mut AML Q6 AML183 61 m FLT3-wt,NPM1-mut AML1 AML1 44 f FLT3-ITD,NPM1-mut AML2 Q59 61 f FLT3-wt,NPM1-mut AML3 AML3 55 m FLT3-ITD,NPM1-mut APL Q1 APL224 70 f APL APL Q2 APL223 54 f APL APL Q3 APL142 66 m APL APL Q4 APL147 45 m APL APL Q5 APL124 32 m APL APL Q6 APL218 46 f APL
Changelog
v2: Objects were slimmed 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.

Seurat v3 object
ASSAYS: AB: Antibody expression data RNA: mRNA expression data BOTH: mRNA and Antibody expression data, concatenated integrated: Antibody and mRNA expression matrices were concatenated and data was integrated across patients using scanorama
DIMENSIONALITY REDUCTION MOFAUMAP: UMAP performed on MOFA dimensions. Display used in the manuscript. Set reduction="MOFAUMAP"in most cases!
Projected MOFA: Multi-OMICS factor analysis to integrate AB and RNA data. MOFA was run on scanorama-integrated data and served as input for clustering and further dimensionality reduction. MOFATSNE: UMAP performed on MOFA dimensions.

METADATA Batch: Source individual (BM1-3, Aged1-3). class: Type of individual (healthy young, healthy old).
Change log: v3: Compared to the previous version of this file, the 3 AML patients were removed. A new object with 15 AML patients has been created: https://doi.org/10.6084/m9.figshare.14780127.v1 v4: Objects were slimmed 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.

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.

Seurat v3 object
ASSAYS: AB: Antibody expression data RNA: mRNA expression data BOTH: mRNA and Antibody expression data, concatenated integrated: Antibody and mRNA expression matrices were concatenated and data was integrated across patients using scanorama
DIMENSIONALITY REDUCTION MOFAUMAP: UMAP performed on MOFA dimensions. Display used in the manuscript. Set reduction="MOFAUMAP"in most cases!
Projected MOFA: Multi-OMICS factor analysis to integrate AB and RNA data. MOFA was run on scanorama-integrated data and served as input for clustering and further dimensionality reduction. MOFATSNE: UMAP performed on MOFA dimensions.

METADATA Batch: Source individual (BM1-3, Aged1-3). class: Type of individual (healthy young, healthy old).
Change log: v3: Compared to the previous version of this file, the 3 AML patients were removed. A new object with 15 AML patients has been created: https://doi.org/10.6084/m9.figshare.14780127.v1 v4: Objects were slimmed 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.

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.

seurat v3 object
ASSAYS:AB: Antibody expression dataRNA: mRNA expression dataBOTH: Antibody and mRNA expression matrices concatenated
DIMENSIONALITY REDUCTIONProjected: Data was projected on the reference dataset MOFAUMAP coordinates.
METADATABatch: Sample1 (Bone marrow) or Sample2 (Blood)
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
Changelogv3: Compared to the previous version of the file, projected UMAP coordinates and projected cell type labels were added.
v4: Objects were slimmed 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.

Seurat v3 object
ASSAYS: AB: Antibody expression data RNA: mRNA expression data integrated: Antibody and mRNA expression matrices were concatenated and data was integrated across patients using scanorama
DIMENSIONALITY REDUCTION MOFA: Multi-OMICS factor analysis to integrate AB and RNA data. MOFA was run on scanorama-integrated data and served as input for clustering and further dimensionality reduction. MOFAUMAP: UMAP performed on MOFA dimensions. Projected: Cell projected into the MOFAUMAP space of a healthy dataset. Display used in the manuscript.

METADATA ct: Cell type Batch: Source individual (AML1-3, AML Q1-Q6, APL Q1-Q6)
Patient Identifier age gender Genotype AML Q1 AML116 71 f FLT3-ITD,NPM1-mut AML Q2 AML327 62 f FLT3-wt,NPM1-mut AML Q3 AML127 56 f FLT3-wt,NPM1-mut AML Q4 AML314 51 m FLT3-ITD,NPM1-mut AML Q5 AML334 78 m FLT3-wt,NPM1-mut AML Q6 AML183 61 m FLT3-wt,NPM1-mut AML1 AML1 44 f FLT3-ITD,NPM1-mut AML2 Q59 61 f FLT3-wt,NPM1-mut AML3 AML3 55 m FLT3-ITD,NPM1-mut APL Q1 APL224 70 f APL APL Q2 APL223 54 f APL APL Q3 APL142 66 m APL APL Q4 APL147 45 m APL APL Q5 APL124 32 m APL APL Q6 APL218 46 f APL
Changelog
v2: Objects were slimmed 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.

R data archive containing the seurat v3 object Integration_200AB

ASSAYS:AB: Antibody expression dataRNA: mRNA expression dataBOTH: Antibody and mRNA expression matrices concatenatedintegrated: Antibody and mRNA expression matrices were concatenated and data was integrated across the blood and bone marrow sample using scanorama
DIMENSIONALITY REDUCTIONMOFA: Multi-OMICS factor analysis to integrate AB and RNA data. MOFA was run on scanorama-integrated data and 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.

METADATABatch: Sample1 (Bone marrow) or Sample2 (Blood)