Table 1.
Selected genes for siRNA knockdown screening
| Subcellular function | NCBI symbol | Is differentially expressed gene (DEG) or protein (DEP)? | NCIB description |
|---|---|---|---|
| Exosome complex mediated degradation of deadenylated mRNA | Dis3 | No DEG/DEP | DIS3 homolog, exosome endoribonuclease and 3′-5′ exoribonuclease |
| mRNA splicing | Mbnl1 | No DEG, Upregulated protein at 5h | muscleblind like splicing factor 1 |
| mRNA splicing | Sf3a2 | No DEG/DEP | splicing factor 3a, subunit 2 |
| mRNA splicing | Snrnp70 | No DEG/DEP | small nuclear ribonucleoprotein 70 (U1) |
| Pyrimidine de novo synthesis | Cad | No DEG/DEP | carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase |
| Pyrimidine de novo synthesis | Dhodh | Upregulated gene at 4 h, no DEP | dihydroorotate dehydrogenase |
| Pyrimidine salvage | Tymp | Upregulated gene at 4 h/NO DEP | thymidine phosphorylase |
| Sphingomyelin synthesis | Col4a3bp | No DEG/DEP | collagen, type IV, alpha 3 (Goodpasture antigen) binding protein |
| Synthesis of complex gangliosides | Plekha8 | No DEG/DEP | pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8 |
| Synthesis of complex gangliosides | Ugcg | Downregulated gene at 2 h, Upregulated gene at 6 h and 8 h, no DEP | UDP-glucose ceramide glucosyltransferase |
| Phosphatidylcholine (PC) synthesis | Pcyt1a | No DEG/DEP | phosphate cytidylyltransferase 1, choline, alpha isoform |
| Phosphatidylethanolamine (PE) synthesis | Pcyt2 | No DEG/DEP | phosphate cytidylyltransferase 2, ethanolamine |
| Cotranslational protein insertion into ER | Srp54a | No DEG/DEP | signal recognition particle 54A |
| Mitochondrial transport | Rhot1 | Downregulated gene at 4 h, no DEP | ras homolog family member T1 |
| Mitochondrial fusion | Mfn2 | No DEG/DEP | mitofusin 2 |
| Mitochondrial translation | Tufm | No DEG/DEP | Tu translation elongation factor, mitochondrial |
| Mitochondrial protein import | Mtx1 | Downregulated gene at 6 h, Upregulated protein at 5 h | metaxin 1 |
| Golgi derived vesicle loading on microtubules, actin-microtubule crosslinking | Macf1 | Downregulated gene at 4 h, Upregulated gene at 6 h, no DEP | microtubule-actin crosslinking factor 1 |
| Vesicle priming during exocytosis | Unc13b | No DEG/DEP | unc-13 homolog B |
| Exocyst-mediated vesicle tethering during exocytosis | Exoc4 | No DEG/DEP | exocyst complex component 4 |
| Exocyst-mediated vesicle tethering during exocytosis | Expc7 | No DEG, Upregulated protein at 5 h | exocyst complex component 7 |
| Clathrin-mediated endocytosis | Ap2m1 | No DEG/DEP | adapter related protein complex 2 subunit mu1 |
| Retromer-mediated endosomal sorting | Snx2 | No DEG/DEP | sorting nexin 2 |
| Retromer-mediated endosomal sorting | Vps35 | No DEG/DEP | VPS35 retromer complex component |
| Microtubule plus-end growth | Mapre1 | Upregulated gene at 6 h, Upregulated protein at 5h | microtubule-associated protein, RP/EB family, member 1 |
| Cytokinesis/neurite pruning/multivesicular body formation | Chmp6 | No DEG, Downregulated protein at 5 h | charged multivesicular body protein 6 |
| Multivesicular body formation | Hgs | No DEG/DEP | HGF-regulated tyrosine kinase substrate |
| Cytokinesis/neurite pruning/multivesicular body formation | Tsg101 | No DEG/DEP | tumor susceptibility gene 101 |
| Tubular endoplasmic reticulum formation | Atl2 | No DEG/DEP | atlastin GTPase 2 |
| Tubular endoplasmic reticulum formation | Rtn1 | No DEG/DEP | reticulon 1 |
| Complement activation | Masp2 | Downregulated gene at 4 h and 6 h, no DEP | mannan-binding lectin serine peptidase 2 |
| Copper transmembrane transport | Atp7b | No DEG/DEP | ATPase, Cu++ transporting, beta polypeptide |
| Insulin mediated glucose import | Slc2a4 | No DEG/DEP | solute carrier family 2 (facilitated glucose transporter), member 4 |
| N-glycan maturation | Man1a2 | Upregulated gene at 6 h, Upregulated protein at 5 h | mannosidase, alpha, class 1A, member 2 |
| Synthesis of non-ATP Nucleoside triphosphates | Nme1 | Upregulated gene at 2 h and 4 h, no DEP | NME/NM23 nucleoside diphosphate kinase 1 |
| Nuclear protein translocation | Nup88 | Upregulated gene at 8 h, no DEP | nucleoporin 88 |
We selected representative genes for the indicated subcellular functions to test the effect of their knockdown on neurite outgrowth. Most of the selected genes were not among the differentially expressed genes (No DEG) or differentially expressed proteins (No DEP) after HU210 treatment of N2A cells.