Table 2.

SDRF representation of the investigation design graph in Figure 3.

Sample ID	Characteristics [Organism]	Characteristics [OrganismPart]	Protocol REF	Extract ID	Protocol REF	Label	Hybridization ID	ArrayDesign REF	ArrayData URI	DerivedArrayData Matrix URI
liver 1	Homo sapiens	liver	P-XMPL-1	Extract 1	P-XMPL-3	Cy3	Hyb 1	SMD-10K	1.txt	FGDM.txt
liver 2	Homo sapiens	liver	P-XMPL-1	Extract 2	P-XMPL-3	Cy3	Hyb 1	SMD-10K	1.txt	FGDM.txt
kidney 1	Homo sapiens	kidney	P-XMPL-1	Extract 3	P-XMPL-3	Cy3	Hyb 2	SMD-10K	2.txt	FGDM.txt
kidney 2	Homo sapiens	kidney	P-XMPL-1	Extract 4	P-XMPL-3	Cy3	Hyb 2	SMD-10K	2.txt	FGDM.txt
brain 1	Homo sapiens	brain	P-XMPL-1	Extract 5	P-XMPL-3	Cy3	Hyb 3	SMD-10K	3.txt	FGDM.txt
brain 2	Homo sapiens	brain	P-XMPL-1	Extract 6	P-XMPL-3	Cy3	Hyb 3	SMD-10K	3.txt	FGDM.txt
				Extract reference	P-XMPL-3	Cy5	Hyb 1	SMD-10K	1.txt	FGDM.txt
				Extract reference	P-XMPL-3	Cy5	Hyb 2	SMD-10K	2.txt	FGDM.txt
				Extract reference	P-XMPL-3	Cy5	Hyb 3	SMD-10K	3.txt	FGDM.txt

Each 'layer' in the graph is represented by an ID column in the spreadsheet, followed by columns for each of the labels. Each path in the graph is represented by one row in the spreadsheet.