|
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]
|
https://www.ncbi.nlm.nih.gov/pubmed/26198319
|
|
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]
|
https://github.com/satijalab/seurat
|
|
Scanorama (online version as of 2019-11-19)
|
[13]
|
https://github.com/brianhie/scanorama
|
|
Harmony (online version as of 2019-11-19)
|
[54]
|
https://github.com/immunogenomics/harmony
|
|
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]
|
http://software.broadinstitute.org/gsea/index.jsp
|
|
Ingenuity Pathway Analysis (IPA, 2019-08-30)
|
QIAGEN
|
https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/
|
