Gene primers in the Qiagen Custom RT2 Profiler PCR Array CAPR11291R
| Gene | Function | RefSeq no. | FC |
|---|---|---|---|
| Adcyap1 | Stimulates cAMP production; upregulated over development (Boeshore et al., 2004; Wang et al., 2007) | NM_016989 | - |
| Akt1 | Downstream of PI3K; critical in neurotrophin-mediated growth and survival (Kaplan and Miller, 2000; Perkinton et al., 2002; Campos et al., 2003) | NM_033230 | ↑ |
| Akt3 | Downstream of PI3K; critical in neurotrophin-mediated growth and survival (as above) | NM_031575 | ↕ |
| ApoE | Involved in CNTF signaling, regulated over development (Fischer, 2012) | NM_138828 | ↓ |
| Arg1 | Downstream from cAMP in survival and regeneration; critical in overcoming myelin inhibition; regulated over development (Cai et al., 2002; Moore and Goldberg, 2011) | NM_017134 | - |
| ATF3 | Transcription factor; interacts with CREB and c-JUN; upregulated after injury, promotes regeneration (Seijffers et al., 2006; Moore and Goldberg, 2011) | NM_012912 | - |
| Bad | Pro-apoptotic protein (Isenmann et al., 2003; Wilson and Di Polo, 2012) | NM_022698 | - |
| Bax | Pro-apoptotic protein (as above) | NM_017059 | ↑ |
| Bcl2 | Anti-apoptotic protein; necessary for neuronal survival; overexpression reduces PCD (Brunet et al., 2001; Campos et al., 2003) | NM_016993 | <2 |
| Bcl2l1 | Anti- or pro-apoptotic protein depending on splice variant (as above) | NM_031535 | - |
| Bcl2l11 | Pro-apoptotic protein; downstream of FOXO transcription factors (as above) | NM_022612 | - |
| BDNF | Promotes RGC survival; axon branching; synaptogenesis (Numakawa et al., 2010) | NM_012513 | ↑ |
| CAMK1 | Phosphorylates CREB; prolongs ERK activation; regulates axon growth (Lonze and Ginty, 2002; Perkinton et al., 2002; Jiao et al., 2005) | NM_134468 | ↓ |
| CAMK2d | Phosphorylates CREB; prolongs ERK activation; regulates axon growth and dendritic architecture; involved in depolarization-induced survival (as above) | NM_012519 | ↕ |
| CAMK2g | Phosphorylates CREB; prolongs ERK activation; regulates axon growth, dendritic architecture, neurite length; involved in depolarization-induced survival (as above) | NM_133605 | ↓ |
| Casp8 | Apoptotic factor; expressed after injury; mediates apoptosis through FOXO1 (Brunet et al., 2001; O’Driscoll et al., 2006; Johnson et al., 2009) | NM_022277 | - |
| Casp9 | Apoptotic factor; activates effector caspases; involved in PCD (as above) | NM_031632 | - |
| Cdc42 | Rho family GTPase; positive regulator of actin dynamics, microtubule formation, growth cone formation, and axon elongation; acts in opposition to RhoA (Zhou and Snider, 2006; Major and Brady-Kalnay, 2007; Hausott et al., 2009) | NM_171994 | ↑ |
| Cdh1 | Adhesion factor; regulates axon growth and patterning (Konishi et al., 2004) | NM_031334 | - |
| CNTFR | Receptor for CNTF; promotes growth and survival (Yip and So, 2000; Lingor et al., 2008) | NM_001003 929 | ↑ |
| CREB1 | Transcription factor; critical for survival and growth signaling (Lonze and Ginty, 2002; Moore and Goldberg, 2011) | NM_031017 | ↑ |
| DCC | Guidance factor; receptor for netrin-1; involved in guidance toward optic disk (Koeberle and Bähr, 2004; Erskine and Herrera, 2007) | NM_012841 | - |
| DCX | Microtubule-associated protein; growth promoting (Blackmore et al., 2010) | NM_053379 | - |
| DSCAM | Guidance factor; involved in self-avoidance (Fuerst et al., 2008,2009) | NM_133587 | <2 |
| EFNA2 | Ephrin A2 ligand; involved in inhibition; expressed in development and after axotomy in adult (O’Leary and Wilkinson, 1999; Cang et al., 2008) | NM_001168 670 | - |
| EGFR | Receptor for EGF; involved in myelin inhibition; required for development of some CNS regions (Hannila and Filbin, 2008; Hausott et al., 2009) | NM_031507 | - |
| ELK1 | Transcription factor; regulates cell cycling; pro-survival effects (Hausott et al., 2009) | XM_001055 949 | - |
| EphA4 | Receptor for Ephrin A and B; involved in inhibition (O’Leary and Wilkinson, 1999; Reber et al., 2004; Lindqvist et al., 2010) | NM_001162 411 | <2 |
| Fos | Involved in regulation of TrkB expression (Chang et al., 2004; Park et al., 2004) | NM_022197 | <2 |
| FOXO3 | Pro-apoptotic transcription factor; inhibited by neurotrophin signaling via Akt and SGK (Brunet et al., 2001) | NM_001106 395 | - |
| Gap43 | Protein required for axon growth (Schaden et al., 1994) | NM_017195 | - |
| GHR | Growth hormone receptor; pro-survival effects on developing RGCs via CREB (Sanders et al., 2008) | NM_017094 | ↓ |
| GSK3B | Influences cytoskeleton assembly; involved in pro-apoptotic signaling; apoptotic function inhibited by Akt (Brunet et al., 2001; Tokuoka et al., 2002; Alabed et al., 2010) | NM_032080 | ↑ |
| HAND1 | Transcription factor, required for sympathetic neuronal survival (Doxakis et al., 2008) | NM_021592 | <2 |
| HAND2 | Transcription factor, required for sympathetic neuronal survival (as above) | NM_022696 | - |
| IGF-1R | Growth factor receptor; promotes RGC survival and growth (Goldberg et al., 2002) | NM_052807 | ↕ |
| Il6R | Cytokine receptor; promotes RGC survival and growth (Cao et al., 2006; Moore and Goldberg, 2011) | NM_017020 | ↑ |
| IL6st | Part of the IL6R complex; promotes RGC survival and growth (as above) | NM_001008 725 | ↓ |
| JAK1 | Component of JAK/STAT signaling cascade; involved in signaling via IL6R, CNTFR, and GHR; regulated in development (Park et al., 2004; Wang et al., 2007) | NM_053466 | <2 |
| JAK2 | Component of JAK/STAT signaling cascade (Park et al., 2004) | NM_031514 | - |
| Jun | Transcription factor; involved in apoptosis, growth, and regeneration (Lu et al., 2003; Tedeschi, 2012) | NM_021835 | - |
| KLF4 | Transcription factor; inhibits axon growth, regulated in development (Moore et al., 2009) | NM_053713 | <2 |
| KLF6 | Transcription factor; promotes axon growth (Veldman et al., 2007; Moore et al., 2009) | NM_031642 | - |
| KLF7 | Transcription factor; promotes axon outgrowth (as above) | NM_001108 800 | ↕ |
| KLF9 | Transcription factor; inhibits axon outgrowth (as above) | NM_057211 | - |
| L1CAM | Cell adhesion molecule, upregulated in axon regeneration (Fischer et al., 2004) | NM_017345 | - |
| LIFR | IL6 class cytokine receptor; neurotrophic factor; promotes survival and growth in RGCs (Goldberg et al., 2002; Moore and Goldberg, 2011; Fischer, 2012) | NM_031048 | - |
| LINGO1 | Part of Nogo receptor complex (Mi et al., 2004; Fu et al., 2008; Hannila and Filbin, 2008) | NM_001100 722 | - |
| MafK | Transcription factor; upregulated after axotomy (Fischer et al., 2004) | NM_145673 | - |
| MAP2k1 | Major neurotrophin signaling pathway (Atwal et al., 2000; Gao et al., 2003; Hausott et al., 2009; Johnson et al., 2009) | NM_031643 | - |
| MAP2k2 | Major neurotrophin signaling pathway (as above) | NM_133283 | ↕ |
| MAPK1 | Kinase involved in MAPK signaling (Kaplan and Miller, 2000; Reichardt, 2006) | NM_053842 | <2 |
| MAPK14 | Kinase involved in both apoptosis and survival signaling; downstream phosphorylation of CREB; possibly involved in neurite outgrowth (as above) | NM_031020 | - |
| MAPK3 | Kinase involved in MAPK signaling (as above) | NM_017347 | ↑ |
| MAPK8 | Kinase involved in pro-apoptotic signaling; inhibits Akt, downstream in p75NTR apoptotic signaling; activates c-Jun; regulates microtubule formation (Kaplan and Miller, 2000; Roux and Barker, 2002; Zhou and Snider, 2006) | XM_341399 | <2 |
| MAPK9 | Kinase involved in pro-apoptotic signaling; involved in developmental apoptosis (Kuan et al., 1999; Le-Niculescu et al., 1999) | NM_017322 | <2 |
| mTOR | Kinase; controls protein synthesis required for axon growth; downstream of PI3K (Park et al., 2008) | NM_019906 | ↓ |
| NFATc3 | Transcription factor; involved in axonal growth; neurotrophins alter activity (Zhou and Snider, 2006; Moore and Goldberg, 2011) | NM_001108 447 | <2 |
| NFATc4 | Transcription factor; involved in axonal growth; neurotrophins alter activity (as above) | NM_001107 264 | <2 |
| Ngfr | p75NTR; low-affinity neurotrophin receptor; pro-neurotrophin receptor; pro- or anti-apoptotic depending on conditions (Kaplan and Miller, 2000; Roux and Barker, 2002) | NM_012610 | - |
| Nptx2 | Role in synaptic plasticity (Fischer et al., 2004) | NM_001034 199 | - |
| Nrxn1 | Involved in synapse formation (Barker et al., 2008) | NM_021767 | ↕ |
| Nrxn2 | Involved in synapse formation (as above) | NM_053846 | - |
| Ntrk2 | TrkB; receptor for BDNF (Atwal et al., 2000; Kaplan and Miller, 2000) | NM_012731 | <2 |
| Optn | Involved in axonal transport, regulated in development (Wang et al., 2007) | NM_145081 | ↑ |
| Pde4b | Enzyme responsible for cAMP hydrolysis; inhibited by neurotrophin signaling (Gao et al., 2003; Hannila and Filbin, 2008) | NM_017031 | - |
| PKCcd | Kinase involved in PI3K and p75NTR/NgR signaling; regulates MAPK activity (Reichardt, 2006; Zhou and Snider, 2006; Major and Brady-Kalnay, 2007) | NM_133307 | - |
| PLCg1 | Phospholipase activated through TrkB; extends MAPK signaling; increases intracellular Ca2+ (Segal, 2003; Zhou and Snider, 2006; Numakawa et al., 2010) | NM_013187 | ↓ |
| POU4F1 | Transcription factor Brn3a; involved in dendritic branching and architecture (Weishaupt et al., 2005; Badea et al., 2009; Voyatzis et al., 2012) | XM_341372 | ↓ |
| POU4F2 | Transcription factor Brn3b; involved in cell-fate determination; critical for RGC differentiation, involved in axonal development (as above) | NM_134355 | - |
| Psip1 | Transcription factor; regulates expression of growth-associated genes; involved in dendritic arborization (Zhao et al., 2008) | NM_175765 | - |
| PTEN | Phosphatase; converts PIP3 to PIP2; inhibits Akt and downstream signaling (Park et al., 2008) | NM_031606 | ↑ |
| Ptk7 | Transcription factor; downstream in PI3K and MAPK pathways; involved in BDNF-induced survival (Chang et al., 2004) | NM_001106 889 | - |
| Rac1 | Rho family GTPase; involved in growth cone mechanics; inhibits RhoA; involved in nasal-temporal crossing (Pearse, 2004; Schiller, 2006; Major and Brady-Kalnay, 2007) | NM_134366 | ↑ |
| RelA | NFkB transcription factor; involved in axonal growth and survival; activated by p75NTR (Moore and Goldberg, 2011) | NM_199267 | - |
| RhoA | GTPase; activates ROCK triggering growth cone collapse; binds to p75NTR (Park et al., 2005; Lingor et al., 2008; Mi, 2008; Hausott et al., 2009) | NM_057132 | ↑ |
| Rock1 | Kinase; downstream of RhoA in mediating growth cone collapse (as above) | NM_031098 | - |
| Rps6 | Ribosomal protein; growth and survival promoting (Sun and He, 2010) | NM_017160 | - |
| Rps6ka1 | Phosphorylates ribosomal Protein s6; activates STATs, CREB; involved in MAPK survival signaling (Lonze and Ginty, 2002; Chang et al., 2004; Koeberle and Bähr, 2004) | NM_031107 | - |
| Rps6ka2 | Phosphorylates ribosomal Protein s6; activates STATs, CREB; involved in MAPK survival signaling (as above) | NM_057128 | <2 |
| Rps6kb1 | Phosphorylates ribosomal Protein s6; downstream of Akt and mTOR (Manning and Cantley, 2007; Park et al., 2008) | NM_031985 | - |
| Rtn4r | Part of NgR-p75NTR signaling complex; mediates inhibitory signaling dependent on cAMP levels and Arg1 activity (Cai et al., 2002; Schwab, 2004; Fu et al., 2008) | NM_053613 | - |
| SGK1 | Kinase; involved in PI3K pathway, similar to Akt; inhibits pro-apoptotic factors, e.g., FOXO3 (Brunet et al., 2001) | NM_019232 | - |
| SOCS3 | Negative regulator of JAK/STAT signaling; knock-out improves regeneration (Sun and He, 2010; Hellström et al., 2011; Fischer, 2012) | NM_053565 | - |
| Sort1 | Pro-neurotrophin receptor; complexes with p75NTR; pro-apoptotic (Jansen et al., 2007; Teng et al., 2010) | NM_031767 | <2 |
| SOX11 | Transcription factor; increases expression of growth-associated molecules (Veldman et al., 2007; Moore and Goldberg, 2011) | NM_053349 | - |
| STAT1 | Activated by STAT3 via JAK/STAT cascade (Moore and Goldberg, 2011; Tedeschi, 2012) | NM_032612 | ↑ |
| STAT3 | Component of JAK/STAT signaling cascade; pro-survival signaling (as above) | NM_012747 | ↑ |
| Stk24 | Kinase; critical for axon regeneration in cultured CNS neurons (mst3B; Lorber et al., 2009) | NM_001127 494 | ↑ |
| Tnfrsf19 | TROY; takes place of p75NTR with LINGO and NgR (Park et al., 2005; Hisaoka, 2006; Mi, 2008) | Unigene: Rn.202731 | - |
| PPIA | Housekeeping gene (commonly used rat housekeeping gene in laboratory) | NM_017101 | - |
| Rpl10a | Housekeeping gene (Hong Cai et al., 2007) | NM_031065 | - |
| HPRT | Housekeeping gene (Vázquez Chona and Vazquez, 2004) | NM_012583 | - |
Brief function, relevant citations, and RefSeq number are listed for each gene. Arrows in the right column indicate a >±2 relative fold change (FC) in gene expression when comparing expression levels between E18/P1 and E15/P0, E18/P1 and E18/P5, or E18/P5 and E15/P0 groups. ↕, relative change in expression, either up or down, depending on pairwise comparison; see Fig. 2B for details. <2, genes with a change in expression <±2; -, genes that failed to amplify in one or more samples, or amplification was evident but only after cycle 45 and therefore discounted.