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Table 1 Summary of the data sets used in this research

From: Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL)

Biospecimen

Name

Details

N

Training or testing

GEO ID

Description

Whole Blood (WB)

AdultMixed

Unfractioned peripheral blood leukocytes (PBL)

6

Training

GSE77797

DNAm profiling of WB samples collected from 6 different healthy adult donors.

 

MethodA

Reconstructed cell mixtures

6

Testing

GSE77797

DNAm profiled in samples consisting of mixtures of CD4T, CD8T, NK, B cells, Monocytes, and Granulocytes, mixed predetermined proportions

 

MethodB

Reconstructed cell mixtures

6

Testing

GSE77797

DNAm profiled in samples consisting of mixtures of CD4T, CD8T, NK, B cells, Monocytes, and Granulocytes, mixed predetermined proportions

 

Liu

Unfractioned peripheral blood leukocytes (PBL)

689

Testing

GSE42861

DNAm profiled in WB samples collected from n=354 rheumatoid arthritis and n=335non-diseased control patients [16]

 

Hannum

Unfractioned peripheral blood leukocytes (PBL)

656

Testing

GSE40279

DNAm profiled in WB samples collected from a total of 656 adults ranging in age from 19–101 years old [29]

Isolated cell types (Reference set)

Granulocytes (Gran)

Purified CD16+ cells

6

Both

GSE35069

DNAm profiling in purified cell types [3]

 

Monocytes (Mono)

Purified CD14+ cells

6

Both

GSE35069

DNAm profiling in purified cell types [3]

 

B cells (Bcell)

Purified CD19+ cells

6

Both

GSE35069

DNAm profiling in purified cell types [3]

 

Natural Killer (NK)

Purified CD56+ cells

6

Both

GSE35069

DNAm profiling in purified cell types [3]

 

CD8T

Purified CD3+CD8+ cells

6

Both

GSE35069

DNAm profiling in purified cell types [3]

 

CD4T

Purified CD3+CD4+ cells

6

Both

GSE35069

DNAm profiling in purified cell types [3]