Table 1

Comparison of different methods and approaches for the analysis of human ES-cell gene expression
	Sperger et al. [1]	Sato et al. [2]	Richards et al. [3]	Abeyta et al. [4]	Zeng et al. [5]

Human ES-cell lines used	H1, H7, H9, H13, H14	H1	HES3, HES4	H9, HSF-1, HSF-6	BG01, BG02
Culture conditions	MEFs	Matrigel	MEFs	MEFs	MEFs
Method of ES-cell isolation	Treatment with collagenase until colonies lifted off the MEFs	Treatment with dispase until cells were free of MEFs	Microdissection to free colonies of MEFs	Mechanical dissection of colonies from MEFs, then collagenase treatment	Trypsinization
Arrays used	Stanford microarrays	Affymetrix arrays (hU133A and mouse U74Av2)	SAGE	Affymetrix arrays (hU133A and hU133B)	Custom 16,659-spot 70-bp oligonucleotide array
Cells compared	hEC, hES and seminoma	hES and published mES [16]	hES and hES and additional SAGE libraries [24]	hES and hES versus published mES [16]	hES and hES versus mES [28]
Primary subtraction method	Somatic and cancer cell lines	Differentiated hES cells	None	None	Pooled human RNA
Software/analysis used	Significance analysis of microarrays (SAM) [25]	dChip and MAS 4.0 (Affymetrix)	Comparison of two SAGE resources with SAGE 2000 [26,27]	MAS 5.0 (Affymetrix)	Gene Pix (Axon Instruments)
Number of genes enriched in human ES cells	1,760	918	8,341	7,385	373
Candidate pluripotency genes*	565	227	192	76	92
Confirmation of gene expression using	RT-PCR	RT-PCR	RT-PCR	Quantitative RT-PCR	RT-PCR

*Candidate pluripotency genes are defined as genes that are found only in all pluripotent cell lines examined in each study. Abbreviations: hEC, human embryonal carcinoma cells; hES, human embryonic stem cells; MEFs, mouse embryonic fibroblasts; mES, mouse embryonic stem cells; RT-PCR, reverse-transcriptase-coupled PCR; SAGE, serial analysis of gene expression.
Pyle et al. Genome Biology 2004 5:235 doi:10.1186/gb-2004-5-8-235