Reagents and tools table
| Reagent/resource | Reference or source | Identifier or catalog number |
|---|---|---|
| Experimental models | ||
| Recombinant DNA | ||
| Antibodies | ||
| Oligonucleotides and other sequence-based reagents | ||
| Chemicals, enzymes, and other reagents | ||
| DMEM/F12 medium | Gibco | 11039 |
| Dithiothreitol (DTT) | AppliChem | A2948 |
| Fetal bovine serum (FBS) | Gibco | 10500 |
| DMSO | Sigma-Aldrich | D8418 |
| PBS | Sigma-Aldrich | D8537 |
| Red Blood Cell Lysis Buffer | Roche | 11814389001 |
| Accutase | Thermo Fisher | 00-4555-56 |
| Chromium Next GEM Single Cell 3’ Kits v3.1 | 10X Genomics | PN-1000121, PN-1000120, PN-1000123 |
| QIAamp® DNA Blood Mini Kit | QIAGEN | 51104 |
| NEBNext® Enzymatic Methyl-seq Kit (Protocol for Large Insert Libraries) | New England Biolabs | E7120 |
| Software | ||
| OTP pipeline | https://gitlab.com/one-touch-pipeline/otp | |
| bwa v.0.7.8 | https://github.com/lh3/bwa | |
| GATK | https://github.com/broadinstitute/gatk | |
| methylCtools v.1.0.0 | https://github.com/hovestadt/methylCtools | |
| EPISCORE | https://github.com/aet21/EpiSCORE | |
| DSS v.2.38 | https://github.com/haowulab/DSS | |
| BisSNP | https://github.com/dnaase/Bis-tools | |
| Cellranger v.3.0.1 | 10X Genomics | |
| Seurat v.3.2.2 | https://github.com/satijalab/seurat | |
| scanpy v.1.6.0 | https://github.com/scverse/scanpy | |
| harmony v.0.0.5 | https://github.com/immunogenomics/harmony | |
| bbknn v.1.4.0 | https://github.com/Teichlab/bbknn | |
| fgsea v.1.24.0 | https://github.com/alserglab/fgsea | |
| Cytoscape v.3.8.2 | https://cytoscape.org/ Shannon et al, 2003 | |
| Other | ||
| 35 µm cell strainer | Falcon | 352235 |
| Neubauer chamber | NanoEnTek | DHC-N01 |
| NovaSeq 6000 Sequencing System | Illumina | |
| ME220 Focused-Ultrasonicator | Covaris | |