干细胞PCR基因芯片可以同时检测与干细胞鉴定、生长和分化相关的84个基因的表达，包括干细胞特异性标记和干细胞分化标记。该芯片同时包括与干细胞维持相关的重要信号通路中的基因。利用实时定量PCR，研究者可以方便并且可信地对与干细胞生物学相关的基因进行同时检测。
Stem Cell Specific Markers: Cell Cycle Regulators: APC, AXIN1, CCNA2, CCND1, CCND2, CCNE1, CDK1, CDC42, EP300, FGF1, FGF2, FGF3, FGF4, MYC, NOTCH2, PARD6A, RB1. Chromosome and Chromatin Modulators: KAT2A, HDAC2, KAT8, KAT7, RB1, TERT. Genes Regulating Symmetric/Asymmetric Cell Division: DHH, NOTCH1, NOTCH2, NUMB, PARD6A. Self-Renewal Markers: HSPA9, KAT8, KAT7, NEUROG2, SOX1, SOX2. Cytokines and Growth Factors: BMP1, BMP2, BMP3, CXCL12, FGF1, FGF2, FGF3, FGF4, GDF2, GDF3, IGF1, JAG1. Genes Regulating Cell-Cell Communication: DHH, DLL1, GJA1, GJB1, GJB2, JAG1. Cell Adhesion Molecules: APC, BGLAP, CD4, CD44, CDH1, CDH2, COL9A1, CTNNA1, CXCL12, NCAM1. Metabolic Markers: ABCG2, ALDH1A1, ALDH2, FGFR1. Stem Cell Differentiation Markers: Embryonic Cell Lineage Markers: ACTC1, ASCL2, FOXA2, PDX1 (IPF1), ISL1, KRT15, MSX1, MYOD1, T. Hematopoietic Cell Lineage Markers: CD3D, CD4, CD8A, CD8B, MME. Mesenchymal Cell Lineage Markers: ACAN (AGC1), ALPI, BGLAP, COL1A1, COL2A1, COL9A1, PPARG. Neural Cell Lineage Markers: CD44, NCAM1, SIGMAR1, S100B, TUBB3. Signaling Pathways Important for Stem Cell Maintenance: Notch Pathway: DLL1, DLL3, DTX1, DTX2, DVL1, EP300, KAT2A, HDAC2, JAG1, NOTCH1, NOTCH2, NUMB. Wnt Pathway: ADAR, APC, AXIN1, BTRC, CCND1, FRAT1, FZD1, MYC, PPARD, WNT1.