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

From: Chipping away at 'stemness'

  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
  1. *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.