PURPOSE Side-population (SP) cells isolated from limbal and conjunctival epithelia derive from cells that are slow bicycling in vivo, a known feature of tissue stem cells. and/or stem cell self renewal (homeodomain genes); (2) cell survival (e.g., CYP1A1 to degrade aromatic genotoxic compounds); (3) cycling rate (e.g., DUSPs and Pax6 to foster slow cycling); and (4) genes whose expression is usually not common in epithelia (e.g., = 4) could not be a full representation of a human population for all genes. The SI ratio filter was waived for those transcripts that had a PPPP/AAAA MAS 5.0 call distribution. From the all- and differentially 1023595-17-6 manufacture expressed transcript lists, we generated corresponding lists of known genes, the all-expressed (AE) and differentially expressed (DE) gene lists, respectively, by removing ESTs and other nonannotated entries and by choosing the transcript that yielded the highest SI for a given gene when more than one transcript representing a single gene existed. In all cases examined, this transcript represented the sequence closer to the 3 (polyA) end of the gene. The Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov/ provided in the public domain name by the National Institute of Allergy or intolerance and Infectious Diseases [NIAID], Bethesda, MD), was used to identify overrepresented entities and biological or molecular processes within the differentially expressed transcripts. DAVID analysis probes each gene list against the corresponding population lists and calculates scores (= 4) were 2.6 and 2.4 pmol/cells for the SP and nSP populations, respectively or between 15 to 30 ng/per experiment. These limited quantities of RNA hindered measurements of RNA purity or origami honesty. This problem was particularly important in this study because the need to trypsinize adherent cells and maintain them in suspension until and during sorting could cause some RNA degradation. 1023595-17-6 manufacture Hence, we relied on the quality control probes included in the microarray (HG-U133A plus 2.0; Affymetrix) to generate a robust retrospective analysis of the effect of the cellular control used on the final quality of the microarray results. The microarray contains three distinct probes for glyceraldehyde-3 phosphodehydrogenase (also represents a cell surface protein present in the myeloid lineage with no FLJ13165 previous association with epithelial cells.18 It has been identified as a marker for myeloid and hepatic-yielding stem cells.19 The fifth gene in Table 3, and sina oculis1 (is 1023595-17-6 manufacture highly expressed in the ocular surface epithelia and may contribute to the stem cell phenotype as a proliferation moderator.24 TABLE 5 Substantially Over- or Underexpressed Homeodomain and Development-Related Genes The highly overexpressed and genes act as dominating negative blockers for the differentiation-inducing helix-loop-helix proteins. expression preserves purified hematopoietic cells ex lover vivo and augments the hematopoietic SP cell population in vivo.25 is critical for long-term repopulating hematopoietic stem-cell maintenance.26 In fact and manifestation may be interrelated. During development, expression is usually enhanced by product activity.27 Within the stem-cellCrelated canonical WNT/ catenin/ TCF pathway,28,29 the DE gene list included only two genes, and gene and of its receptor, FZD5. The pathways associated with, and effects of noncanonical WNTs are poorly comprehended.31 When acting as an inhibitor, has been shown to foster a slow-cycling status that stabilizes the hematopoietic stem cell phenotype.32 Furthermore, WNT5a may act as an activator or inhibitor of the (canonical) catenin/TCF 1023595-17-6 manufacture signaling depending on receptor context.33 Hence, the noncanonical classification of Wnt5a does not preclude a relevant role.