Table 2 mRNAs differentially expressed in FACS-isolated Tis21-GFP+ versus Tis21-GFP− S-phase NPCs of E14.5 mouse neocortex.
From: Neural stem and progenitor cells shorten S-phase on commitment to neuron production
Gene category | Gene (abbr.) | Gene (full name) | Function | FC | P -value |
|---|---|---|---|---|---|
Validation | Eomes | Eomesodermin homolog (Xenopus laevis), Tbr2 | Proneural gene, BP marker | +8.7 | 0.015 |
Neurog2 | Neurogenin 2 | Proneural gene | +4.4 | 0.014 | |
Insm1 | Insulinoma-associated 1 | Panneurogenic, BP-genic gene | +4.3 | 0.031 | |
Fabp7 | Fatty acid-binding protein 7 | Neural stem cell maintenance | −2.9 | 0.014 | |
Nes | Nestin | Intermediate filament protein, AP marker | −2.3 | 0.026 | |
Cell-cycle regulation | Cdkn1c | Cyclin-dependent kinase inhibitor 1C (p57) | Antiproliferative gene | +3.0 | 0.022 |
Ccng2 | Cyclin G2 | Mid/late S-phase cyclin | +2.4 | 0.007 | |
Rb1 | Retinoblastoma 1 | G1/S transition regulator | +2.4 | 0.013 | |
Cdk2ap1 | Cdk2 (cyclin-dependent kinase 2)-associated protein 1 | Cdk2 inhibitor | +1.7 | 0.011 | |
Cdc25a | Cell division cycle 25 homolog A (Schizosaccharomyces pombe) | Activator of S-phase progression, regulator of DNA checkpoints | +1.6 | 0.027 | |
Cdk4 | Cyclin-dependent kinase 4 | G1/S transition | +1.5 | 0.012 | |
Erf | Ets2 repressor factor | Repressor of c-Myc and cdc2 | −3.0 | 0.039 | |
Cdkl2 | Cyclin-dependent kinase-like 2 | Cyclin-dependent kinase | −2.5 | 0.042 | |
Fbxw7 | F-box and WD-40 domain protein 7 | Subunit of ubiquitin ligase complex promoting degradation of cell cycle-positive regulators | −1.9 | 0.019 | |
DNA replication and repair | E2f1 | E2F transcription factor 1 | Positive regulator for S-phase progression | +2.2 | 0.016 |
Fen1 | Flap structure-specific endonuclease 1 | Positive regulator of Okazaki fragment maturation and base excision repair | +2.0 | 0.039 | |
Fancf | Fanconi anemia, complementation group F | Positive regulator of translesion synthesis | +1.7 | 0.031 | |
Rnaseh2b | Ribonuclease H2, subunit B | Positive regulator of Okazaki fragment | +1.5 | 0.016 | |
Top2a | Topoisomerase (DNA) II alpha | Regulator of DNA checkpoints, relaxing supercoiled DNA | +1.5 | 0.046 | |
Tdg | Thymine DNA glycosylase | Initiator of base excision repair | +1.3 | 0.041 | |
Chd1l | Chromodomain helicase DNA-binding protein 1-like | Positive regulator of chromatin relaxation for DNA repair | −2.2 | 0.031 | |
Parp16 | Poly(ADP-ribose) polymerase family, member 16 | Positive regulator of DNA repair | −1.9 | 0.042 | |
Chromatin remodeling | Gadd45g | Growth arrest and DNA-damage-inducible 45 gamma | DNA demethylase | +4.1 | 0.032 |
Cbx2 | Chromobox homolog 2 (Drosophila Pc class) | Polycomb repressive complex subunit | +1.9 | 0.007 | |
Phc2 | Polyhomeotic-like 2 (Drosophila) | Polycomb repressive complex subunit | +1.6 | 0.020 | |
Kdm1a | Lysine (K)-specific demethylase 1A | Histone modifier | +1.6 | 0.042 | |
Hdac2 | Histone deacetylase 2 | Histone modifier | +1.5 | 0.030 | |
H3f3b | H3 histone, family 3B | Chromatin component | +1.5 | 0.031 | |
Kdm2b | Lysine (K)-specific demethylase 2B | Histone modifier | +1.5 | 0.046 | |
Brd3 | Bromodomain containing 3 | Histone modifier | +1.4 | 0.026 | |
Bmi1 | Bmi1 polycomb ring finger oncogene | Polycomb repressive complex subunit | +1.3 | 0.033 | |
Sin3a | Transcriptional regulator, SIN3A (yeast) | Regulator of histone modification | +1.3 | 0.040 | |
Hils1 | Histone H1-like protein in spermatids 1 | Chromatin component | −3.6 | 0.010 | |
Hmga2 | High-mobility group AT-hook 2 | Chromatin component | −3.4 | 0.037 | |
Pcgf5 | Polycomb group ring finger 5 | Polycomb repressive complex subunit | −2.1 | 0.049 | |
Mbd2 | Methyl-CpG-binding domain protein 2 | Histone modifier | −1.9 | 0.024 | |
Neurogenesis | Neurod1 | Neurogenic differentiation 1 | Proneural gene | +5.5 | 0.017 |
Insc | Inscuteable homolog (Drosophila) | Regulator of mitotic spindle orientation | +5.3 | 0.014 | |
Dll3 | Delta-like 3 (Drosophila) | Notch ligand | +4.7 | 0.015 | |
Insm2 | Insulinoma-associated 2 | Presumptive panneurogenic, BP-genic gene | +4.2 | 0.030 | |
Hes6 | Hairy and enhancer of split 6 (Drosophila) | Positive regulator of neurogensis | +3.3 | 0.012 | |
Numbl | Numb-like | Notch inhibitor | +2.1 | 0.013 | |
Ascl1 | Achaete-scute complex homolog 1 (Drosophila) | Positive regulator of neurogensis | +2.1 | 0.028 | |
Notch3 | Notch gene homolog 3 (Drosophila) | Neural stem cell maintenance | −4.1 | 0.012 | |
Wnt7a | Wingless-related MMTV integration site 7A | Neural stem cell maintenance | −3.8 | 0.025 | |
Sox8 | SRY-box containing gene 8 | Oligodendrocyte specification | −3.8 | 0.027 | |
Notch2 | Notch gene homolog 2 (Drosophila) | Neural stem cell maintenance | −3.6 | 0.019 | |
Fgfr2 | Fibroblast growth factor receptor 2 | Neural stem cell maintenance | −2.6 | 0.016 | |
Dtx4 | Deltex 4 homolog (Drosophila) | Positive regulator of Notch | −2.6 | 0.049 | |
Sox1 | SRY-box containing gene 1 | Stem cell maintenance | −2.2 | 0.031 | |
Fgf18 | Fibroblast growth factor 18 | Neural stem cell maintenance | −2.0 | 0.049 | |
Tle1 | Transducin-like enhancer of split 1 | Neural stem cell maintenance | −1.9 | 0.033 | |
Jag1 | Jagged 1 | Notch ligand | −1.6 | 0.015 |
