Comparative analysis with 3 different approaches
Researcher . | Stem cell population/baseline cell population . | RNA amplification . | Microarray, no. of ESTs characterized/uncharacterized . | Overlap of HSC-enriched genes with our CD34+CD38--enriched genes . | Overlap of HSC-enriched genes with our SDf-enriched genes . |
|---|---|---|---|---|---|
| Own data | HCB: CD34+CD38-/CD34+CD38+ HCB: SDF/FDF | In vitro transcription (2 rounds) | cDNA: Human Transcriptome Microarray, >15 000/51 145 | 27 | 355 |
| Ivanova et al9 | HFL: CD34+CD38-/Lin+ MBM: Lin-c-Kit+-Scal+ Rholow/Lin+ MFL: Lin-AA4.1+ c-Kit+ Scal+/Lin+ | In vitro transcription (2 rounds) | Oligonucleotide microarrays (Affymetrix) HG-U95 A, B, C, D, E: >10 000/60 000 MG-U74v2 A, B, C: >6000/36 000 | 5 (RBPMS, R-RAS, PRDM1, EMCN-PENDING, CASP12) | 38 (HOXA9, RBPMS, FZD6, JAK3, PRDM1, CYSLT1, P2RY5, DNMT3A, UTRN, NFKB1A, CIQR1, CHN2, CPXM1, LMYC1, MYCN, EZNF, TC10, KCNMB1, SV2, FZD8, ITGAV, MMP7, NCAM2, ADA, KLF12, SOX4, LANO, FHL1, MANBA, SSBP2, MAFB, JM1, ZNF43, ETV6, CLECSF2, SIGIRR-PENDING, H2-DMA, GIG1) |
| Ramalho-Santos et al10 | MBM: Hoechst33342low Scal+ c-Kit+ CD34-Lin-/Lin+ | In vitro transcription (2 rounds) | Oligonucleotide microarrays (Affymetrix) U74Av2 A: > 6000/12 000 | 5 (RBPMS, R-RAS, HSP40, NCKAP1, CASP12) | 15 (HOXA9, RBPMS, MDR1, JAK3, ITM2, GNG11, TC10, LTB, MYCN, STXBP3, ITM3, NAALADASEL, GALNT3, HLA-DMA, CKIP-1) |
| Terskikh et al15 | MBM: c-Kit+ Thy1.1low Scal+Lin-/average expression level of 7 populations | SMART-PCR (19 cycles) | cDNA Atlas 1.2 (Clontech) 1200 | 0 | 5 (HOXA9, FZD6, MDR1, ITGB2, PCLG2) |
Researcher . | Stem cell population/baseline cell population . | RNA amplification . | Microarray, no. of ESTs characterized/uncharacterized . | Overlap of HSC-enriched genes with our CD34+CD38--enriched genes . | Overlap of HSC-enriched genes with our SDf-enriched genes . |
|---|---|---|---|---|---|
| Own data | HCB: CD34+CD38-/CD34+CD38+ HCB: SDF/FDF | In vitro transcription (2 rounds) | cDNA: Human Transcriptome Microarray, >15 000/51 145 | 27 | 355 |
| Ivanova et al9 | HFL: CD34+CD38-/Lin+ MBM: Lin-c-Kit+-Scal+ Rholow/Lin+ MFL: Lin-AA4.1+ c-Kit+ Scal+/Lin+ | In vitro transcription (2 rounds) | Oligonucleotide microarrays (Affymetrix) HG-U95 A, B, C, D, E: >10 000/60 000 MG-U74v2 A, B, C: >6000/36 000 | 5 (RBPMS, R-RAS, PRDM1, EMCN-PENDING, CASP12) | 38 (HOXA9, RBPMS, FZD6, JAK3, PRDM1, CYSLT1, P2RY5, DNMT3A, UTRN, NFKB1A, CIQR1, CHN2, CPXM1, LMYC1, MYCN, EZNF, TC10, KCNMB1, SV2, FZD8, ITGAV, MMP7, NCAM2, ADA, KLF12, SOX4, LANO, FHL1, MANBA, SSBP2, MAFB, JM1, ZNF43, ETV6, CLECSF2, SIGIRR-PENDING, H2-DMA, GIG1) |
| Ramalho-Santos et al10 | MBM: Hoechst33342low Scal+ c-Kit+ CD34-Lin-/Lin+ | In vitro transcription (2 rounds) | Oligonucleotide microarrays (Affymetrix) U74Av2 A: > 6000/12 000 | 5 (RBPMS, R-RAS, HSP40, NCKAP1, CASP12) | 15 (HOXA9, RBPMS, MDR1, JAK3, ITM2, GNG11, TC10, LTB, MYCN, STXBP3, ITM3, NAALADASEL, GALNT3, HLA-DMA, CKIP-1) |
| Terskikh et al15 | MBM: c-Kit+ Thy1.1low Scal+Lin-/average expression level of 7 populations | SMART-PCR (19 cycles) | cDNA Atlas 1.2 (Clontech) 1200 | 0 | 5 (HOXA9, FZD6, MDR1, ITGB2, PCLG2) |
Mouse-human homolog genes were determined as described in “Materials and methods.”
HCB indicates human cord blood; HFL, human fetal liver; MBM, mouse bone marrow; SDF, slow-dividing fraction within CD34+CD38- cell population; FDF, fast-dividing fraction in CD34+CD38- cell population; MFL, mouse fetal liver.