Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets

Maden, Sean K.; Kwon, Sang Ho; Huuki-Myers, Louise A.; Collado-Torres, Leonardo; Hicks, Stephanie C.; Maynard, Kristen R.

doi:10.1186/s13059-023-03123-4

Table 4 Cell scale factor estimates from the literature, with focus on deconvolution studies that use sequencing references. Values for blood cell types are from the SimBu R package (v1.2.0), and values for brain cell types are from Table 1 in (3). The Scale factor value (column 3) can be used in existing deconvolution algorithms leading to less biased results for estimating cell composition

From: Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets

Cell type	Tissue	Scale factor value	Scale factor type	Scale factor data source	Citation(s)
Glial	Brain	91	Cell area	osmFISH	[3, 80]
Neuron	Brain	123	Cell area	osmFISH	[3, 80]
Glial	Brain	180	Nuclear mRNA	osmFISH	[3, 80]
Neuron	Brain	198	Nuclear mRNA	osmFISH	[3, 80]
Glial	Brain	12,879	Library size	expression	[1, 3]
Neuron	Brain	18,924	Library size	expression	[1, 3]
B cells	Multiple	65.66	Median expression	Housekeeping gene expression	[36, 74]
Macrophages	Multiple	138.12	Median expression	Housekeeping gene expression	[36, 74]
Macrophages (M2)	Multiple	119.35	Median expression	Housekeeping gene expression	[36, 74]
Monocytes	Multiple	130.65	Median expression	Housekeeping gene expression	[36, 74]
Neutrophils	Multiple	27.74	Median expression	Housekeeping gene expression	[36, 74]
NK cells	Multiple	117.72	Median expression	Housekeeping gene expression	[36, 74]
T cells CD4	Multiple	63.87	Median expression	Housekeeping gene expression	[36, 74]
T cells CD8	Multiple	70.26	Median expression	Housekeeping gene expression	[36, 74]
T regulatory cells	Multiple	72.55	Median expression	Housekeeping gene expression	[36, 74]
Dendritic cells	Multiple	140.76	Median expression	Housekeeping gene expression	[36, 74]
T cells	Multiple	68.89	Median expression	Housekeeping gene expression	[36, 74]
B cells	Multiple	0.40	Intensity	FACS	[40, 74]
Macrophages	Multiple	1.42	Intensity	FACS	[40, 74]
Monocytes	Multiple	1.42	Intensity	FACS	[40, 74]
Neutrophils	Multiple	0.13	Intensity	FACS	[40, 74]
NK cells	Multiple	0.44	Intensity	FACS	[40, 74]
T cells	Multiple	0.40	Intensity	FACS	[40, 74]
T cells CD4	Multiple	0.40	Intensity	FACS	[40, 74]
T cells CD8	Multiple	0.40	Intensity	FACS	[40, 74]
T helper cells	Multiple	0.40	Intensity	FACS	[40, 74]
T regulatory cells	Multiple	0.40	Intensity	FACS	[40, 74]
B cells	Multiple	20837.57	Intensity	FACS	[35, 74]
Monocytes	Multiple	22824.32	Intensity	FACS	[35, 74]
Neutrophils	Multiple	9546.74	Intensity	FACS	[35, 74]
NK cells	Multiple	21456.91	Intensity	FACS	[35, 74]
T cells CD4	Multiple	14262.07	Intensity	FACS	[35, 74]
T cells CD8	Multiple	10660.95	Intensity	FACS	[35, 74]
Plasma cells	Multiple	325800.99	Intensity	FACS	[35, 74]
Dendritic cells	Multiple	57322.18	Intensity	FACS	[35, 74]

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