Table 1.
RNA expression datasets analyzed in this study.
| Dataset ID (in this study) | Biological source | Description | Use in this study | Reference |
|---|---|---|---|---|
| FUSCC | TNBC tumor | Bulk RNASeq from 286 female Chinese patients with primary TNBC | Identification of gene networks and estimation of their cell-type specificity (via CIBERSORT) | (27) |
| TCGA TNBC | TNBC tumor | Bulk RNASeq from 162 female TCGA patients with TNBC | Validation of gene networks | (21) |
| LINCS | cancer cell lines | Library of RNASeq of cancer cell lines before and after drug exposure (more than 8000 compounds listed) | Drug-induced gene expression signatures for selected opioid agonists and antagonists | (28) |
| cts_PBMC | PBMCs | Tissue-specific RNASeq from 79 human-derived physiologically normal tissues | Validation of cell-type specificity of gene networks | (29) |
| sc_TIL_TNBC | TNBC intratumoral immune cells | Single-cell RNASeq of intratumoral immune cells in TNBC | Validation of cell-type specificity of gene networks | (30) |
| sc_morphine_PBMC | PBMCs | Single-cell RNASeq of PBMCs from 7 opioid-dependent individuals and 7 controls as well as control cells dosed with morphine | Morphine gene response signature in PBMCs | (31) |
| cts_morphine_CD8 | CD8+ T-cells | Cell-type specific RNASeq of CD8+ T-cells from 5 donors, before and after dosing of the cells with morpine | Morphine gene response signature in CD8+ T-cells | (32) |
| sc_ICI_TIL_TNBC | TNBC intratumoral immune cells | Single-cell RNASeq of intratumoral immune cells from 22 TNBC patients who received anti-PD-L1 therapy | Anti-PD-L1 gene response signature in TNBC intratumoral immune cells | (22) |
| bulk_ketamine_PBMC | PBMCs | Bulk RNASeq of whole blood (PBMCs) from 26 patients with treatment-resistant depression, before and after ketamine treatment, and 21 controls | Ketamine gene response signature in PBMCs | (33) |
FUSCC, Fudan University Shanghai Cancer Center; LINCS, Library of Integrated Network-Based Cell Signatures; PBMC, Peripheral blood mononuclear cells (lymphocytes (T-cells, B-cells, NK cells), monocytes, dendritic cells); RNASeq, Ribonucleic acid sequencing; TCGA, The Cancer Genome Atlas; TNBC, triple-negative breast cancer.
Note that there are three different types of RNASeq represented here: bulk, cell-type specific (cts), and single-cell (sc). Bulk RNASeq sequences RNA extracted from a large number of cells (mixed together), hence representing average gene expression across thousands of tumor cells. Cell-type specific RNASeq is bulk RNASeq, but of a specific cell-type that has been isolated from the rest. Single-cell RNASeq involves sequencing of RNA extracted from individual cells.