Table 1.
Genes Investigated by Custom NanoString Panel
| Gene type |
Gene name |
Gene symbol |
|---|---|---|
| Glial genes | Glial fibrillary acidic protein |
Gfap |
| S100 protein | S100b | |
| Neuronal genes | Synaptophysin | Syp |
| RNA binding protein (NeuN) | Rbfox3 | |
| Macrophage genes | CD68 antigen | Cd68 |
| Adhesion G protein-coupled receptor E1 (F4/80) | Adgre1 | |
| Phagocytosis genes | CD36 antigen | CD36 |
| C-type lectin domain family 7 | Clec7A | |
| Collectin subfamily member 12 | Colec12 | |
| Ficolin A | Fcn1 | |
| Ficolin Ba | Fcn2 | |
| Multiple EGF-like-domains 10 | Megf10 | |
| Platelet endothelial aggregation receptor 1 | Pear1 | |
| Engulfment adaptor PTB domain | Gulp1 | |
| Stabilin 2 | Stab2 | |
| Milk fat globule-EGF factor 8 | Mfge8 | |
| Tubby-like protein 1 | Tulp1 | |
| Antigen processing and presentation genes | Cathepsin B | Ctsb |
| Class II transactivator | Ciita | |
| Histocompatibility 2, class II antigen A, β1 | H2-Ab1 | |
| Histocompatibility 2, class II, locus Dma | H2-Dma | |
| Cathepsin L | Ctsl | |
| CD40 antigen | Cd40 | |
| CD80 antigen | Cd80 | |
| CD86 antigen | Cd86 | |
| Lysosomal-associated membrane protein 1 | Lamp1 | |
| Lysosomal-associated membrane protein 2 | Lamp2 | |
| Toll-like receptor 2 | Tlr2 | |
| Toll-like receptor 4 | Tlr4 | |
| Cytokines | Interleukin 1 | Il1 |
| Interleukin 2 | Il2 | |
| Interleukin 4 | Il4 | |
| Interleukin 6a | Il6 | |
| Interleukin 8a | Il8 | |
| Interleukin 12A | Il12a | |
| Interleukin 12B | Il12b | |
| Interleukin 18 | Il18 | |
| Interleukin 23, α subunit p19 | Il23a | |
| Transforming growth factor β | Tgfb1 | |
| Tumor necrosis factor α | Tnf | |
| Interferon γ | Ifng | |
| Lymphocyte activation gene 3 | Lag3 | |
| Lymphotoxin A | Lta | |
| Lymphotoxin B | Ltb | |
| Neutrophil cytosolic factor 1 | Ncf1 | |
| Internal reference genes | Alanyl-tRNA synthetase | Aars |
| Ankyrin repeat and SOCS box-containing 10 | Asb10 | |
| Coiled-coil domain containing 127 | Ccdc127 | |
| CCR4-NOT transcription complex, subunit 10 | Cnot10 | |
| Casein kinase 2, α prime polypeptide | Csnk2a2 | |
| Family with sequence similarity 104, member A | Fam104a | |
| Glucuronidase, β | Gusb | |
| Leucyl-tRNA synthetase | Lars | |
| Mitochondrial tRNA translation optimization 1 | Mto1 | |
| Suppressor of Ty 7-like | Supt7l | |
| Transcriptional adaptor 2B | Tada2b | |
| TATA box binding protein | Tbp | |
| X-prolyl aminopeptidase (aminopeptidase P) 1, soluble | Xpnpep1 |
NOTE. Selected genes in pathways related to phagocytosis, antigen processing and presentation, and cytokines.
CCR4, C-C Motif Chemokine Receptor 4; EGF, Epidermal growth factor; PTB, Polypyrimidine Tract Binding Protein; SOCS, Suppressor of cytokine signaling; tRNA, transfer ribonucleic acid. Glial, neuronal, macrophage, and internal reference genes were used as controls.
a
Genes that did not pass NanoString panel quality control and were not included in the analysis. Glial, neuronal, macrophage, and internal reference genes were used as controls.