Table 2 Orthogonal cell type amount measurements used for bulk transcriptomics deconvolution. Table describes the name (column 1) and a description (column 2) of the type of measurement, the type of assay used to capture the measurement (column 3), and example citations for these measurements (column 4)

Fluorescent in situ hybridization (FISH)

Labeling and imaging of DNA-based cell type markers

In situ labeling, imaging

[3, 56]

Immunohistochemistry (IHC)

Antibody-based cell marker labeling and imaging

In situ labeling, imaging

[40, 57]

Immunofluorescence (IF)

Antibody-based fluorescent labeling of cell markers

In situ labeling, imaging

[3, 58]

In vitro cell mixtures

Sequencing of manually mixed cells from dissociated bulk tissues or cell lines

Bulk RNA-seq

[30, 31, 38, 44, 45, 59]

Fluorescence-activated cell sorting (FACS)

Sequencing of cells isolated by cytometric sorting

Flow cytometry; bulk RNA-seq

[6, 35, 40]

Genetic panel

DNA marker-based differentiation of tissues, esp. tumor from non-tumor

Genetic marker assay; microarray

[39, 60]

DNA methylation

Deconvolution using DNA methylation cell type markers

Microarray; bisulfite sequencing

[3, 42, 50, 61,62,63]

Hematoxylin and eosin staining

Clinical tissue slide staining procedure

In situ staining; imaging

[42, 56]