Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference |
Identifiers | Additional information |
|---|---|---|---|---|
| Peptide, recombinant protein | Tn5 | doi: https://doi.org/10.1101/615179 | ||
| Chemical compound, drug | NEBNext High-Fidelity 2 × PCR Master Mix | NEB | Cat# M0541L | |
| Chemical compound, drug | RNasin Ribonuclease Inhibitor | Promega | Cat# N211B | |
| Chemical compound, drug | DRAQ7 | Cell Signaling | Cat# 7406 | |
| Commercial assay or kit | Chromium Single Cell 3′ Library Construction Kit v3 | 10x Genomics | Cat# 1000075 | |
| Commercial assay or kit | Chromium Single-Cell B Chip Kit | 10x Genomics | Cat# 1000153 | |
| Commercial assay or kit | Chromium i7 Multiplex Kit, 96 rxns | 10x Genomics | Cat# 120262 | |
| Chemical compound, drug | SPRISelect reagent | Beckman Coulter | Cat# B23319 | |
| Software, algorithm | Cell Ranger software package v3.0.2 | 10x Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) | Software | |
| Software, algorithm | Seurat v3.1.4 | https://satijalab.org/seurat/ doi:10.1016/j.cell.2019.05.031 | RRID:SCR_016341 | |
| Software, algorithm | DoubletFinder |
https://github.com/chris-mcginnis-ucsf/DoubletFinder
doi:10.1016/j.cels.2019.03.003 |
RRID:SCR_018771 | |
| Software, algorithm | GraphPad Prism version 8.0.0 | www.graphpad.com | RRID:SCR_002798 | |
| Software, algorithm | Trim galore (v.0.4.4) |
https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ | RRID:SCR_011847 | |
| Software, algorithm | BWA (v.0.7.1) |
http://bio-bwa.sourceforge.net/ doi:10.1093/bioinformatics/btp324 | RRID:SCR_010910 | Software |
| Software, algorithm | Samtools (v. 1.10) |
http://www.htslib.org/ doi:10.1093/bioinformatics/btp352 | RRID:SCR_002105 | Software |
| Software, algorithm | Picard | http://broadinstitute.github.io/picard/ | RRID:SCR_006525 | Software |
| Software, algorithm | scanpy (v.1.4.4.post1) |
https://github.com/theislab/scanpy | RRID:SCR_018139 | Software |
| Software, algorithm | Harmony (v. 0.1.0) | https://github.com/immunogenomics/harmony doi:10.1038/s41592-019-0619-0 | Software | |
| Software, algorithm | Cicero (v. 1.4.4) | https://github.com/cole-trapnell-lab/cicero-release doi:10.1016/j.molcel.2018.06.044 | Software | |
| Software, algorithm | liftOver | https://genome.ucsc.edu/cgi-bin/hgLiftOver | RRID:SCR_018160 | Software |
| Other | gnomAD v3 | http://gnomad.broadinstitute.org/ doi:10.1038/s41586-020-2308-7 | RRID:SCR_014964 | Database |
| Other | JASPAR 2020 | http://jaspar.genereg.net doi:10.1093/nar/gkz1001 | RRID:SCR_003030 | Database |
| Software, algorithm | FIMO (v. 4.12.0) | http://meme-suite.org/ doi:10.1093/bioinformatics/btr064 | RRID:SCR_001783 | Software |
| Software, algorithm | deltaSVM | http://www.beerlab.org/deltasvm/ doi:10.1038/ng.3331 | ||
| Software, algorithm | MuSiC (v.0.1.1) | https://github.com/xuranw/MuSiC doi:10.1038/s41467-018-08023-x | ||
| Software, algorithm | Python | https://www.python.org/ | RRID:SCR_008394 | |
| Software, algorithm | R (v.3.5.1) | https://www.r-project.org/ | RRID:SCR_001905 | |
| Software, algorithm | Go (v. 1.12.1) | https://golang.org/ | RRID:SCR_017096 | |
| Software, algorithm | NumPy (v.1.16.1) | https://numpy.org/ | RRID:SCR_008633 | python library |
| Software, algorithm | Scikit-learn (v. 0.20.1) | https://scikit-learn.org/stable/ | RRID:SCR_002577 | python library |
| Software, algorithm | seaborn (v. 0.9.0) | https://seaborn.pydata.org/api.html | RRID:SCR_018132 | python library |
| Software, algorithm | MatPlotLib (v.0.9.0) | http://matplotlib.sourceforge.net | RRID:SCR_008624 | python library |
| Software, algorithm | ATACdemultiplex (v. 0.46.12) | https://gitlab.com/Grouumf/ATACdemultiplex/ | suite of softwares written in GO for snATAC analysis | |
| Software, algorithm | edgeR (v. 3.22.5) | http://bioconductor.org/packages/release/bioc/html/edgeR.html doi:10.1093/bioinformatics/btp616 | RRID:SCR_012802 | R library |
| Software, algorithm | Matrix (v.1.2–15) | https://cran.r-project.org/web/packages/Matrix/index.html | R library | |
| Software, algorithm | Stringr (v. 1.4.0) | https://www.rdocumentation.org/packages/stringr/versions/1.4.0 | R library | |
| Software, algorithm | Cicero (v. 1.0.14) | https://www.bioconductor.org/packages/release/bioc/html/cicero.html doi:10.1016/j.molcel.2018.06.044 | R library | |
| Software, algorithm | HOMER (v4.11.1) | http://homer.ucsd.edu/homer/download.html doi:10.1016/j.molcel.2010.05.004 | RRID:SCR_010881 | Perl package |
| Software, algorithm | rGREAT (v. 1.20) | https://www.bioconductor.org/packages/release/bioc/html/rGREAT.html for GREAT: doi:10.1038/nbt.1630 | for GREAT: RRID:SCR_005807 |
R library |