Table 1 Comparison of different methods and approaches for the analysis of human ES-cell gene expression
| Â | 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 |