Table 1. List of datasets constituting the collection.

Title	Platforms	Diseases	Number of sample	Experiments	GEO ID	References
Interaction of bone marrow stroma and monocytes: bone marrow stromal cell lines cultured with monocytes	Affymetrix	Healthy	8	In vitro	GSE10595	37
Monocyte gene expression profiling in familial combined hyperlipidemia and its modification by atorvastatin treatment	Affymetrix	Familial combined hyperlipidemia	9	In vitro	GSE11393	38
Performance comparison of Affymetrix and Illumina microarray technologies	Affymetrix	Acute coronary syndrome	10	Ex vivo	GSE11430	39
Gene expression profiling in pediatric meningococcal sepsis reveals dynamic changes in NK-cell and cytotoxic molecules	Affymetrix	Meningococcal sepsis	41	Ex vivo	GSE11755	N/A
Effect of interferon-gamma on macrophage differentiation and response to Toll-like receptor ligands	Affymetrix	Healthy	10	In vitro	GSE11864	40
Human monocyte and dendritic Cell Subtype Gene Arrays	Affymetrix	Healthy	8	Ex vivo	GSE11943	41
Microarray analysis of human monocytes infected with Francisella tularensis	Affymetrix	Healthy	14	In vitro	GSE12108	42
Human blood monocyte profile in Ventilator-Associated Pneumonia patients	Affymetrix	Pneumonia	60	Ex vivo	GSE12838	N/A
Quercetin supplementation and CD14+ monocyte gene expression	Affymetrix	Healthy	6	Ex vivo	GSE13899	43
Effects of PMN-Ectosomes on human macrophages	Affymetrix	Healthy	16	In vitro	GSE14419	N/A
Homogeneous monocytes and macrophages from hES cells following coculture-free differentiation in M-CSF and IL-3	Affymetrix	Healthy	9	Ex vivo	GSE15791	44
Expression data from human macrophages	Affymetrix	Healthy	38	In vitro	GSE16385	45
Transcriptional profiling of CD16+ and CD16- peripheral blood monocytes from healthy individuals	Affymetrix	Healthy	8	Ex vivo	GSE16836	32
COPD-Specific Gene Expression Signatures of Alveolar Macrophages as well as Peripheral Blood Monocytes Overlap and Correlate with Lung Function	Affymetrix	Chronic obstructive pulmonary disease	12	Ex vivo	GSE16972	46
Loss-of-function mutations in REP-1 affect intracellular vesicle transport in fibroblasts and monocytes of CHM patients	Affymetrix	Choroideremia	15	Ex vivo	GSE17549	47
Effect of two weeks erythropoietin treatment on monocyte transcriptomes of cardiorenal patients	Illumina	Cardiorenal syndrome	48	Ex vivo	GSE17582	N/A
Comparison of gene expression profiles between human monocyte subsets	Affymetrix	Healthy	6	Ex vivo	GSE18565	48
Subpopulations of CD163 positive macrophages are classically activated in psoriasis	Illumina	Psoriasis	58	Ex vivo	GSE18686	49
Mycobacterium tuberculosis Chaperonin 60.1 has Bipolar Effects on Human peripheral blood-derived Monocytes	Affymetrix	Healthy	21	In vitro	GSE18794	N/A
Blood Transcriptional Profiles of Active TB (Separated cell)	Illumina	Tuberculosis	44	Ex vivo	GSE19443	11
Filaria induced monocyte dysfunction and its reversal following treatment	Affymetrix	Filariasis	14	Ex vivo	GSE2135	50
Ubiquinol-induced gene expression signatures are translated into reduced erythropoiesis and LDL cholesterol levels in humans	Affymetrix	Healthy	6	Ex vivo	GSE21351	51
Monocyte vs Macrophage Study	Affymetrix	Healthy	6	In vitro	GSE22373	52
Monocyte gene expression patterns distinguish subjects with and without atherosclerosis	Illumina	Carotid atherosclerosis	95	Ex vivo	GSE23746	N/A
Deconvoluting Early Post-Transplant Immunity Using Purified Cell Subsets Reveals Functional Networks Not Evident by Whole Blood Analysis	Affymetrix	Kidney transplantation	179	Ex vivo	GSE24223	53
Cooperative and redundant signaling of leukotriene B4 and leukotriene D4 in human monocytes	Affymetrix	Healthy	10	In vitro	GSE24869	54
Gene expression profiling of the classical (CD14++CD16-), intermediate (CD14++CD16+) and nonclassical (CD14+CD16+) human monocyte subsets	Illumina	Healthy	24	Ex vivo	GSE25913	34
Direct Cell Conversion of Human Fibroblasts to Monocytic phagocytes by Forced Expression of Monocytic Regulatory Network Elements	Illumina	Dermatomyositis	15	Ex vivo	GSE27304	N/A
cMyb and vMyb in human monocytes	Affymetrix	Healthy	6	In vitro	GSE2816	55
Temporal transcriptional changes in human monocytes following acute myocardial infarction: The GerMIFs monocyte expression study	Illumina	Acute myocardial infarction	76	Ex vivo	GSE28454	N/A
mRNA expression profiling of human immune cell subset (Roche)	Affymetrix	Healthy	47	Ex vivo	GSE28490	56
mRNA expression profiling of human immune cell subsets (HUG)	Affymetrix	Healthy	33	Ex vivo	GSE28491	56
Changes in gene expression profiles in patients with 5q- syndrome in CD14+ monocytes caused by lenalidomide treatment	Illumina	5q- syndrome	17	Ex vivo	GSE31460	N/A
Genome-wide analysis of lupus immune complex stimulation of purified CD14+ monocytes and how this response is regulated by C1q	Illumina	Healthy	8	In vitro	GSE32278	57
Transcriptome analysis of circulating monocytes in obese patients before and three months after bariatric surgery	Illumina	Obesity	48	Ex vivo	GSE32575	58
CD4 on human monocytes	Affymetrix	Healthy	6	In vitro	GSE32939	59
Peripheral Blood Monocyte Gene Expression in Recent-Onset Type 1 Diabetes	Illumina	Type 1 Diabetes	22	Ex vivo	GSE33440	60
Traffic-related Particulate Matter Upregulates Allergic Responses by a Notch-pathway Dependent Mechanism	Affymetrix	Healthy	16	In vitro	GSE34025	N/A
Human monocyte activation with NOD2L vs. TLR2/1L	Affymetrix	Healthy	45	In vitro	GSE34156	61
Bacillus anthracis' lethal toxin induces broad transcriptional responses in human peripheral monocyte	Affymetrix	Healthy	8	In vitro	GSE34407	62
Gene expression profiles of human blood classical monocytes (CD14++CD16-), CD16 positive monocytes (CD14+16++ and CD14++CD16+), and CD1c+ CD19- dendritic cells	Affymetrix	Healthy	9	Ex vivo	GSE34515	N/A
Genome-wide analysis of monocytes and T cells' response to interferon beta	Illumina	Healthy	12	In vitro	GSE34627	63
Highly pathogenic influenza virus inhibit Inflammatory Responses in Monocytes via Activation of the Rar-Related Orphan Receptor Alpha (RORalpa)	Affymetrix	Healthy	12	In vitro	GSE35283	N/A
Transcriptome profiles of human monocyte and dendritic cell subsets	Illumina	Healthy	49	Ex vivo	GSE35457	64
Influenza virus A infected monocytes	Illumina	Healthy	6	In vitro	GSE35473	65
PGE2-induced OSM expression	Affymetrix	Chronic wound	6	Ex vivo	GSE36995	66
Inflammatory Expression Profiles in Monocyte to Macrophage Differentiation amongst Patients with Systemic Lupus Erythematosus and Healthy Controls with and without an Atherosclerosis Phenotype	Illumina	Systemic lupus erythematosus	72	Ex vivo	GSE37356	N/A
New insights into key genes and pathways involved in the pathogenesis of HLA-B27-associated acute anterior uveitis	Affymetrix	Acute anterior uveitis	6	In vitro	GSE37588	N/A
Analysis of blood myelomonocytic cells from RCC patients	Illumina	Renal cell carcinoma	8	Ex vivo	GSE38424	67
Nanotoxicogenomic study of ZnO and TiO2 responses	Illumina	Healthy	90	In vitro	GSE39316	N/A
Macrophage Microvesicles Induce Macrophage Differentiation and miR-223 Transfer	Affymetrix	Healthy	24	In vitro	GSE41889	68
TREM-1 is a novel therapeutic target in Psoriasis	Affymetrix	Psoriasis	15	In vitro	GSE42305	69
Comparison study between Uremic patient with Healthy control	Affymetrix	Chronic kidney disease	6	Ex vivo	GSE43484	N/A
Microarray analysis of IL-10 stimulated adherent peripheral blood mononuclear cells	Affymetrix	Healthy	8	In vitro	GSE43700	70
Monocytes and Dendritic cells stimulated by 13 human vaccines and LPS	Illumina	Vaccination	128	In vitro	GSE44721	36
Gene expression profile of human monocytes stimulated with all-trans retinoic acid (ATRA) or 1,25a-dihydroxyvitamin D3 (1,25D3)	Affymetrix	Healthy	12	In vitro	GSE46268	71
Transcriptome analysis of blood monocytes from sepsis patients	Illumina	Sepsis	44	Ex vivo	GSE46955	72
Tumor-educated circulating monocytes are powerful specific biomarkers for diagnosis of colorectal cancer	Illumina	Colorectal cancer	93	Ex vivo	GSE47756	73
Similarities and differences between macrophage polarized gene profiles	Illumina	Healthy	12	In vitro	GSE49240	74
The effect of cell subset isolation method on gene expression in leukocytes.	Illumina	Healthy	50	Ex vivo	GSE50008	N/A
Transcriptome analysis of HIV-infected peripheral blood monocytes	Illumina	HIV	86	Ex vivo	GSE50011	75
Gene expression profiles in T-lymphocytes and Monocytes of participants of the Tour de France 2005	Affymetrix	Healthy	66	Ex vivo	GSE5105	N/A
Effects of exercise on gene expression level in human monocytes	Affymetrix	Healthy	24	Ex vivo	GSE51835	76
T helper lymphocyte- and monocyte-specific type I interferon (IFN) signatures in autoimmunity and viral infection.	Affymetrix	Autoimmune diseases	36	Ex vivo	GSE51997	77
Longitudinal comparison of monocytes from an HIV viremic vs avirmeic state	Affymetrix	HIV	16	Ex vivo	GSE5220	78
Expression data from monocytes and monocyte derived macrophages	Affymetrix	Healthy	12	In vitro	GSE52647	N/A
Transcriptome analysis of primary monocytes from HIV+ patients with differential responses to therapy	Illumina	HIV	14	Ex vivo	GSE52900	79
Human blood monocyte response to IL-17A in culture	Affymetrix	Healthy	6	In vitro	GSE54884	N/A
Divergent genome wide transcriptional profiles from immune cell subsets isolated from SLE patients with different ancestral backgrounds	Illumina	Systemic lupus erythematosus	208	Ex vivo	GSE55447	80
Cell Specific Expression & Pathway Analyses Reveal Novel Alterations in Trauma-Related Human T-Cell & Monocyte Pathways	Affymetrix	Trauma patients	42	Ex vivo	GSE5580	81
Immune Variation Project (ImmVar) [CD14]	Affymetrix	Healthy	485	Ex vivo	GSE56034	N/A
Transcriptomics of human monocytes	Illumina	Healthy	1202	Ex vivo	GSE56045	82
Effect of vitamin D treatment on human monocyte	Affymetrix	Healthy	16	In vitro	GSE56490	N/A
Monocytes of patients with familial hypercholesterolemia show alterations in cholesterol metabolism	Affymetrix	Hypercholesterolemia	23	Ex vivo	GSE6054	83
Gene expression data from CD14++ CD16- classical monocytes from healthy volunteers and patients with pancreatic ductal adenocarcinoma	Affymetrix	Pancreatic ductal adenocarcinoma	12	Ex vivo	GSE60601	N/A
Activation of the JAK/STAT pathway in Behcet's Disease	Affymetrix	Behcet’s disease	29	Ex vivo	GSE61399	N/A
Alarmins MRP8 and MRP14 induce stress-tolerance in phagocytes under sterile inflammatory conditions	Illumina	Sterile inflammation	12	In vitro	GSE61477	N/A
GM-CSF induced gene-regulation in human monocytes	Affymetrix	Healthy	6	In vitro	GSE63662	84
Treatment of human monocytes with TLR7 or TLR8 agonists	Affymetrix	Healthy	9	In vitro	GSE64480	85
Restricted Dendritic Cell and Monocyte Progenitors in Human Cord Blood and Bone Marrow	Illumina	Healthy	36	Ex vivo	GSE65128	86
Interleukin-1- and Type I Interferon-Dependent Enhanced Immunogenicity of an NYVAC-HIV-1 Env-Gag-Pol-Nef Vaccine Vector with Dual Deletions of Type I and Type II Interferon-Binding Proteins	Illumina	Vaccination	20	In vitro	GSE65412	N/A
Comparative analysis of monocytes from healthy donors, patients with metastatic breast cancer, sepsis or tuberculosis.	Illumina	Breast cancer and Bacterial infection	13	Ex vivo	GSE65517	87
Expression data from intermediate monocytes from healthy donors and autoimmune uveitis patients	Affymetrix	Autoimmune uveitis	21	Ex vivo	GSE66936	88
Induction of Dendritic Cell-like Phenotype in Macrophages during Foam Cell Formation	Affymetrix	Healthy	22	In vitro	GSE7138	89
Genome Wide Gene Expression Study of Circulating Monocytes in human with extremely high vs. low bone mass	Affymetrix	Healthy	26	Ex vivo	GSE7158	N/A
Genomic profiles for human peripheral blood T cells, B cells, natural killer cells, monocytes, and polymorphonuclear cells: comparisons to ischemic stroke, migraine, and Tourette syndrome	Affymetrix	Healthy	18	Ex vivo	GSE72642	90
Expression data from monocytes of individuals with different collateral flow index CFI	Affymetrix	Coronary artery disease	160	Ex vivo	GSE7638	91
Leukotriene D4 induces gene expression in human monocytes through cysteinyl leukotriene type I receptor	Affymetrix	Healthy	8	In vitro	GSE7807	92
Gene expression profile during monocytes to macrophage differentiation	Affymetrix	Healthy	9	In vitro	GSE8286	N/A
Toll-like receptor triggering of a vitamin D-mediated human antimicrobial response	Affymetrix	Healthy	50	In vitro	GSE8921	93
TRAIL Is a Novel Antiviral Protein against Dengue Virus	Affymetrix	Dengue	10	In vitro	GSE9378	N/A
Gene Expression-Based High Throughput Screening: APL Treatment with Candidate Compounds	Affymetrix	Leukemia	24	Ex vivo	GSE976	94
Innate immune responses to TREM-1 activation	Affymetrix	Healthy	11	In vitro	GSE9988	95