Table 4.
Summary of materials and reagents with suppliers and product numbers.
| Reagent or resource | Source | Identifier |
|---|---|---|
| Consumables | ||
| Polystyrene Petri dishes | VWR | 25384-088 |
| Stainless steel disposable scalpels | Integra | 4-420 |
| 2 ml 1.44 mm ceramic bead tubes | Bertin | P000912-LYSK0-A |
| 40 μM FlowMi Cell Strainers | SP Bel-Art | 136800040 |
| RNase OUT Ribonuclease Inhibitor | Invitrogen | 10777-019 |
| 5 ml round-bottom tube | Falcon | REF 352058 or REF 352063 |
| DAPI (10 μg/ml) | Sigma Aldrich | D9542 |
| RNase away | ||
| 1,000 μl wide-bore pipet tips | Sigma-Aldrich | AXYT1005WBC |
| 1.5 ml LoBind tubes | VWR | CA80077-232 |
| Single-cell commercial assay | ||
| Chromium Next GEM Chip G Single Cell Kit, 16 rxns | 10X Genomics | 1000127 |
| Dual Index Kit TT Set A,96rxn | 10X Genomics | 1000215 |
| Chromium Next GEM Single Cell 3′Kit v3.1, 4 rxns | 10X Genomics | 1000269 |
| Library Construction Kit, 4 rxns-1000196 | 10X Genomics | 1000196 |
| Tube, Dynabeads MyOne SILANE | 10X Genomics | 2000048 |
| 10X Chromium Controller | 10X Genomics | 1000202 |
| Equipment | ||
| Neubauer Hemocytometer | VWR | 15170-208 |
| Minilys Homogenizer | Bertin | |
| FACSaria Fusion | BD | |
| ST 40R Centrifuge | Sorvall | |
| TX-750 Rotor | Thermo Fisher Scientific | |
| Buffers | ||
| Nuclei EZ lysis buffer with RNase inhibitor | Invitrogen | 10777019 |
| Nuclei lysis buffer 0.1X Nuclei EZ lysis buffer in 1X PBS with 0.2 U/μl RNase inhibitor | ||
| Nuclei wash and resuspension buffer | ||
| 1X PBS, 1.5% BSA, 0.2 U/μl RNase inhibitor, 10 μg/ml | ||
| DAPI | ||
| Software and algorithms | ||
| CellRanger | 10X Genomics | Version 6.1.2 |
| STAR | Dobin et al (2013) | Version 2.7.2a |
| R | R Core | Version 4.1.2 |
| Rstudio | R Core | Version 1.4.1106 |
| Seurat | Hao et al (2021) | Version 4.1.0 |