Stem Cell Genome Anatomy Project
HSC - Princeton/UPenn SCGAP Group
  Project Target cell(s) Species Target organ Differentiation state Isolation method Key experimental systems Approach to gene identification Additional Approaches
  1   Hematopoietic stem and progenitor cells human bone marrow multipotent stem cells & oligopotential progenitors FACS stem and progenitor cell purification in vitro assays, stromal cell line cultures, NOD/SCID assays, in utero sheep assays EST sequencing of normalized and/or subtracted libraries, microarrays qRT-PCR
  2   Hematopoietic stem and progenitor cells human umbilical cord blood multipotent stem cells & oligopotential progenitors FACS stem and progenitor cell purification in vitro assays, stromal cell line cultures, NOD/SCID assays, in utero sheep assays EST sequencing of normalized and/or subtracted libraries, microarrays qRT-PCR
  3   Hematopoietic stem and progenitor cells human mobilized peripheral blood multipotent stem cells & oligopotential progenitors FACS stem and progenitor cell purification in vitro assays, stromal cell line cultures, NOD/SCID assays, in utero sheep assays EST sequencing of normalized and/or subtracted libraries, microarrays qRT-PCR
  4   Hematopoietic stem and progenitor cells human fetal liver multipotent stem cells & oligopotential progenitors FACS stem and progenitor cell purification in vitro assays, stromal cell line cultures, NOD/SCID assays, in utero sheep assays EST sequencing of normalized and/or subtracted libraries, microarrays qRT-PCR
Liver, HSC-Baylor SCGAP
  Project Target cell(s) Species Target organ Differentiation state Isolation method Key experimental systems Approach to gene identification Additional Approaches
  1   Adult Liver stem cells mouse liver unknown Cell sorting on dye efflux and cell surface markers Transplantation to liver using FAH -/- mice
  1. Affymetrix microarray
  2. Suppressive subtractive hyb., concatenation and sequencing (SSH-CCS)
  
  2   Immortal mouse embryonic liver cells mouse liver multipotent progenitors
  1. Proliferation
  2. In vivo cell morphology
 Well-characterized growth factor cocktail to induce lineage-specific differentiation Affymetrix and cDNA microarray  
  3   Hematopoietic stem cells mouse bone marrow and fetal liver stem cells Cell sorting on dye efflux and cell surface markers Bone marrow transplantation
  1. Affymetix microarray
  2. SSH-CCS
  
Urologic Epithelial Stem Cell GAP
  Project Target cell(s) Species Target organ Differentiation state Isolation method Key experimental systems Approach to gene identification Additional Approaches
  1   Prostate Epithelial Stem Cells human prostate progenitor basal cells, intermediate cells, differentiated luminal cells cell sorting in vitro cell culture system of sorted cells cDNA microarray, EST sequencing of sorted cell libraries Immunohisto-chemistry of CD antibodies, Proteomics to identify secreted stromal factors
  2   Bladder Epithelial Stem Cells human bladder progenitor basal cells, intermediate cells, differentiated urothelial cells cell sorting in vitro cell culture system of sorted cells cDNA microarray, EST sequencing of sorted cell libraries Immunohisto-chemistry of CD antibodies, Proteomics to identify secreted stromal factors
Kidney-Stem Cell GAP
  Project Target cell(s) Species Target organ Differentiation state Isolation method Key experimental systems Approach to gene identification Additional Approaches
  1   Identification of genes involved in nephron induction and branching Mouse Kidney Embryonic uteric tree tip Vs branch FACS Ret/GFP+ve Uteric tree tip cells Vs GFP+ve cells from kidneys of HoxB7-GFP transgenic mice cDNA/ oligo microarray In situ hybridisation/ Bioinformatic screen for secreted and trans-membrane proteins
  Identification of genes involved in nephron induction and branching Mouse Kidney Metanephric mesenchyme Vs uteric tree FACS Metanephric mesenchyme (GFP-ve) and uteric tree (GFP+ve) from hox7b-GFP transgenic mice. cDNA/ oligo microarray In situ hybridisation/ Bioinformatic screen for secreted and trans-membrane proteins
                Testing of lead secreted molecules in mimCD3 cell differentiation assay
  Temporal expression analysis of the developing kidney 10.5dpc-newborn) Mouse kidney Dissection metanephroi to kidney Vs common RNA reference staged tissues from wild type mice cDNA/ oligo microarray Bioinformatic screen for secreted and trans-membrane proteins/ In situ hybridisation
  2   Defining genes expressed in metanephric mesenchyme Vs adjacent intermediate mesoderm mouse liver metanephric mesenchyme Vs adjacent intermediate mesoderm Dissection staged tissues from wild type mice cDNA/ oligo microarray Bioinformatic screen for secreted and trans-membrane proteins/ In situ hybridisation
                Generation of antibodies to TM proteins, isolation of candidate progenitor populations + screening repair potential by engraftment and explant assays
  3   Expression profiling of renal sub-compartments Mouse Kidney renal interstitial cells, renal macrophages, cap condensates and podocytes Primary culture and FACS wild type mice for interstitial cells, Transgenic: Fms-GFP (macrophages), Nephrin-GFP (Cap condensates) -GFP(podocytes) cDNA/oligo array In situ hybridisation/ Bioinformatic screen for secreted and trans-membrane proteins
  Promoting differentiation of ES cells towards a renal fate Human   Differentiation of ES cell to metanephric mesenchyme Culturing with secreted molecules identified in projects 1-3 Differentiation of NIH registered ES01-06 cell lines In situ hybridisation RT-PCR
  4   Promoting differentiation of ES cells towards a renal fate Mouse   Differentiation of ES cell to metanephric mesenchyme Culturing with secreted molecules identified in projects 1-3 Differentiation of Mouse ES cell- embryoid body cultures In situ hybridisation RT-PCR
Gut-Stem Cell GAP
  Project Target cell(s) Species Target organ Differentiation state Isolation method Key experimental systems Approach to gene identification Additional Approaches
  1   SiEP (Small Intestinal Epithelial Progenitors) mouse small intestine multipotent stem cells & oligopotential progenitors LCM Gnotobiotic transgenic mice lacking Paneth cells allowing isolation of clustered progenitors EST sequencing of normalized libraries qRT-PCR
                oligonucleotide microarrays
  2   GEP (Gastric Epithelial Progenitors) mouse stomach multipotent stem cells & oligopotential progenitors LCM Gnotobiotic transgenic mice lacking parietal cells leading to expanded progenitor population EST sequencing of normalized libraries qRT-PCR
Comparative Hematopoietic Stem Cell GAP
  Project Target cell(s) Species Target organ Differentiation state Isolation method Key experimental systems Approach to gene identification Additional Approaches
  1   Mouse Hemangioblasts and Hematopoietic Stem Cells mouse Mouse Cultured ES cells hemangioblasts and multipotent stem cells Fluorescent Assisted Cell Sorting In vitro differentiation of murine ES cells bearing a surface marker of truncated inactive human CD4 in the SCL/tal-1 locus EST sequencing of normalized libraries Whole-mount in situ hybridization analysis of sequenced ESTs, gene knockout, and comparative genomic analysis of gene regulatory elements.
                oligonucleotide and chip microarrays
  2   Zebrafish Hemangioblast and Hematopoietic Stem Cells Zebrafish Zebrafish AGM (Aorta-Gonad-Mesonephros) hemangioblasts and multipotent stem cells Fluorescent Assisted Cell Sorting LMO-2-GFP transgenic zebrafish embryos EST sequencing of normalized libraries Whole-mount in situ hybridization analysis of sequenced ESTs, gene knockdown and knockout, and comparative genomic analysis of gene regulatory elements.
National Institutes of Health Department of Health and Human Services National Institute of Diabetes and Digestive and Kidney Diseases