Table 1.

Data sets used in this study

ID	Platform	Number regular probes	Number negative controls	Experiment description
1	MouseWG-6 V1.1	46 657	1603	Six cell types: hematopoietic stem cells, CMPs, GMPs, pro DC precursors, neutrophils and macrophages. Number of arrays per cell type: 4, 2, 1, 3, 1 and 3, respectively.
2	MouseWG-6 V1.1	46 657	1603	Two cell types: wild type and Aire knockout MHCIIhi mTECs. Number of arrays per cell type: 3.
3	MouseWG-6 V2	45 281	936	Three cell types: pro DC precursors, neutrophils and macrophages. Number of arrays per cell type: 9, 3 and 3, respectively.
4	MouseWG-6 V2	45 281	936	Four cell types: hematopoietic stem cells, CMPs, GMPs and MEPs. Number of arrays per cell type: 3.
5	HumanWG-6 V1	47 312	1517	Six conditions: MCF7 and Jurkat samples were mixed at six different proportions (see Figure 4a). Number of arrays per condition: 2.
6	HumanWG-6 V1	47 312	1517	Four conditions: Universal Human Reference RNA(UHRR) and Human Brain Reference RNA(HBRR) were mixed at four different proportions (see Figure 4b). Number of arrays per condition: 5. Published in ref. (15)
7	HumanWG-6 V2	48 687	1374	Six conditions: three subtypes of T lymphocytes taken from two patients infected with hepatitis C virus. Number of arrays per condition: 1. Published in ref. (16)
8	HumanHT-12	48 799	759	Twelve samples. Bone marrow from seven malaria-infected and five uninfected donors. Number of arrays per sample: 1.
9	HumanWG-6 V3	48 803	759	Four cell types: Lin−CD49fhiEpCAM−, Lin−CD49f−EpCAM−, Lin−CD49f−EpCAM+ and Lin−CD49f+EpCAM+ mammary subpopulations. Number of arrays per cell type: 3. Published in ref. (17)