List of genes measured by real-time PCR
| Genes . | Accession no. . | Markers . | Reference . |
|---|---|---|---|
| CD19 | NM 001770.3 | B-cell | Additional lineage marker |
| CDK2 | NM 001798.2 | Cell cycle control | Glas et al16 |
| CD47 | NM 001777.3 | Macrophage | Additional lineage marker |
| CD11D (ITGAD) | NM 005353.2 | Macrophage | Additional lineage marker |
| TNFSF13B | NM 006573.3 | Macrophage | Dave et al2 |
| ACTN1 | NM 001102.2 | Macrophage | Dave et al2 |
| CD68 | NM 001251 | Macrophage | Additional lineage marker |
| CCR1 | NM 001295.2 | Macrophage activation | Glas et al16 |
| FCGR1A (CD64) | NM 000566.2 | Macrophage and dendritic cells | Dave et al2 |
| C3AR1 | NM 004054 | Macrophage and dendritic cells | Dave et al2 |
| Sep-10 | NM 144710.2 | Macrophage and dendritic cells | Dave et al2 |
| LGMN | NM 005606.5 | Macrophage and dendritic cells | Dave et al2 |
| TLR5 | NM 003268.3 | Macrophage and dendritic cells | Dave et al2 |
| MAPK1 | NM 002745.4 | Mitogen-activated protein kinase 1 | Glas et al16 |
| CXCL12 | NM 000609.4 | Reactive infiltrate of T cells and macrophage | Glas et al16 |
| TSPAN7 | NM 004615.2 | Reactive infiltrate of T cells and macrophage | Glas et al16 |
| CD3D | NM 000732.3 | Reactive infiltrate of T cells and macrophage | Glas et al16 |
| NEK2 | NM 002497.2 | Signal transduction marker | Glas et al16 |
| CD2 | NM 001767.2 | T cell | Glas et al16 |
| CD4 | NM 000616.2 | T cell | Additional lineage marker |
| CD5 | NM 014207.2 | T cell | Additional lineage marker |
| CD25 (IL2RA) | NM 000417.1 | T cell | Additional lineage marker |
| ITK | NM 005546.3 | T cell | Dave et al2 |
| CD69 | NM 001781.1 | T cell | Glas et al16 |
| LEF1 | NM 016269.2 | T cell | Dave et al2 |
| STAT4 | NM 003151.2 | T cell | Dave et al2 |
| CD6 | NM 006725.2 | T cell | Additional lineage marker |
| CD7 | NM 006137.6 | T cell | Dave et al2 |
| CD8B1 | NM 172213.1 | T cell | Dave et al2 |
| CCL3 | NM 002983.1 | T-cell and macrophage activation | Glas et al16 |
| CCL5 | NM 002985.2 | T-cell and macrophage activation | Glas et al16 |
| CCL8 | NM 005623.2 | T-cell and macrophage activation | Glas et al16 |
| ILF3 | NM 012218.2 | T-cell and macrophage activation | Glas et al16 |
| GEM | NM 005261.2 | T-cell and macrophage activation | Glas et al16 |
| AKAP12 | NM 005100.2 | T-cell and macrophage activation | Glas et al16 |
| Beta actin | NM 001101 | Housekeeping gene | Housekeeping gene |
| Ribosomal S9 | U14971 | Housekeeping gene | Housekeeping gene |
| IF2b | U23028 | Housekeeping gene | Housekeeping gene |
| GAP | NM 002046 | Housekeeping gene | Housekeeping gene |
| Genes . | Accession no. . | Markers . | Reference . |
|---|---|---|---|
| CD19 | NM 001770.3 | B-cell | Additional lineage marker |
| CDK2 | NM 001798.2 | Cell cycle control | Glas et al16 |
| CD47 | NM 001777.3 | Macrophage | Additional lineage marker |
| CD11D (ITGAD) | NM 005353.2 | Macrophage | Additional lineage marker |
| TNFSF13B | NM 006573.3 | Macrophage | Dave et al2 |
| ACTN1 | NM 001102.2 | Macrophage | Dave et al2 |
| CD68 | NM 001251 | Macrophage | Additional lineage marker |
| CCR1 | NM 001295.2 | Macrophage activation | Glas et al16 |
| FCGR1A (CD64) | NM 000566.2 | Macrophage and dendritic cells | Dave et al2 |
| C3AR1 | NM 004054 | Macrophage and dendritic cells | Dave et al2 |
| Sep-10 | NM 144710.2 | Macrophage and dendritic cells | Dave et al2 |
| LGMN | NM 005606.5 | Macrophage and dendritic cells | Dave et al2 |
| TLR5 | NM 003268.3 | Macrophage and dendritic cells | Dave et al2 |
| MAPK1 | NM 002745.4 | Mitogen-activated protein kinase 1 | Glas et al16 |
| CXCL12 | NM 000609.4 | Reactive infiltrate of T cells and macrophage | Glas et al16 |
| TSPAN7 | NM 004615.2 | Reactive infiltrate of T cells and macrophage | Glas et al16 |
| CD3D | NM 000732.3 | Reactive infiltrate of T cells and macrophage | Glas et al16 |
| NEK2 | NM 002497.2 | Signal transduction marker | Glas et al16 |
| CD2 | NM 001767.2 | T cell | Glas et al16 |
| CD4 | NM 000616.2 | T cell | Additional lineage marker |
| CD5 | NM 014207.2 | T cell | Additional lineage marker |
| CD25 (IL2RA) | NM 000417.1 | T cell | Additional lineage marker |
| ITK | NM 005546.3 | T cell | Dave et al2 |
| CD69 | NM 001781.1 | T cell | Glas et al16 |
| LEF1 | NM 016269.2 | T cell | Dave et al2 |
| STAT4 | NM 003151.2 | T cell | Dave et al2 |
| CD6 | NM 006725.2 | T cell | Additional lineage marker |
| CD7 | NM 006137.6 | T cell | Dave et al2 |
| CD8B1 | NM 172213.1 | T cell | Dave et al2 |
| CCL3 | NM 002983.1 | T-cell and macrophage activation | Glas et al16 |
| CCL5 | NM 002985.2 | T-cell and macrophage activation | Glas et al16 |
| CCL8 | NM 005623.2 | T-cell and macrophage activation | Glas et al16 |
| ILF3 | NM 012218.2 | T-cell and macrophage activation | Glas et al16 |
| GEM | NM 005261.2 | T-cell and macrophage activation | Glas et al16 |
| AKAP12 | NM 005100.2 | T-cell and macrophage activation | Glas et al16 |
| Beta actin | NM 001101 | Housekeeping gene | Housekeeping gene |
| Ribosomal S9 | U14971 | Housekeeping gene | Housekeeping gene |
| IF2b | U23028 | Housekeeping gene | Housekeeping gene |
| GAP | NM 002046 | Housekeeping gene | Housekeeping gene |
TaqMan primers and probes for each gene are detailed in Table S1. For each gene, the reference from which it was selected is given (details are provided in references); additional lineage markers selected are indicated as such.