Reagents | |||
Dispase II (neutral protease, grade II) | Sigma-Aldrich | 04942078001 | |
Collagenase D, from Clostridium histolyticum | Sigma-Aldrich | 11088866001 | |
Commercial kits | |||
Chromium Single Cell 3' Library & Gel Bead Kit v2 | 10X Genomics | CG00052 (protocol) | |
Chromium Single Cell 3' Library & Gel Bead Kit v3 | 10X Genomics | CG000183 (protocol) | |
Deposited data | |||
Human ligand-receptor database | [43] | ||
Human scRNA-seq dataset | This paper | GSE143704 | |
Mouse scRNA-seq dataset | [29] | GSE143437 | |
Software packages and algorithms | |||
Cell Ranger 3.1.0 (July 24, 2019) | 10X Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest | |
Seurat 3.1.0 | [14] | ||
Scanorama (online version as of 2019-11-19) | [13] | ||
Harmony (online version as of 2019-11-19) | [54] | ||
biomaRt 2.43.1 (online version as of 2020-01-08) | [64] | https://bioconductor.org/packages/release/bioc/html/biomaRt.html | |
Gene Set Enrichment Analysis (4.0.3) | [65] | ||
Ingenuity Pathway Analysis (IPA, 2019-08-30) | QIAGEN | https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/ |