| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Chemicals, peptides, and recombinant proteins | ||
| Tris-HCl (1 M)∗ | Sigma | T2194-100ML |
| NaCl# | Sigma | S9888-500g |
| MgCl2 (1 M) # | Thermo Fisher Scientific | AM9530G |
| BSA (10%)# | Sigma | A1595-50ML |
| Tween-20 (10%)# | Bio-Rad | 161-0781 |
| NP40 Substitute (10%)# | Sigma | 98379 |
| Nuc Free Water# | Thermo Fisher Scientific | AM9932 |
| Digitonin (5%)∗ | Thermo Fisher Scientific | BN2006 |
| Nuclei Pure Prep Nuclei Isolation Kit∗ | Sigma | NUC-201 |
| Chromium Next GEM Single Cell ATAC Library Kit v1.1∗ | 10× Genomics | PN-1000163 (store at −20°C) |
| Chromium Next GEM Single Cell ATAC Gel Bead Kit v1.1∗ | 10× Genomics | PN-1000159 (store at −80°C) |
| Single Index Kit N Set A∗ | 10× Genomics | PN-1000212 |
| DynabeadsTM MyOneTM SILANE∗ | 10× Genomics | PN-2000048 (store at 4°C) |
| Recovery Agent∗ | 10× Genomics | 220016 |
| Partitioning Oil∗ | 10× Genomics | 2000190 |
| Gasket∗ | 10× Genomics | 370017 |
| Chromium Next GEM Chip H∗ | 10× Genomics | 2000180 |
| Bleach (Pure Bright Liquid Germicidal Ultra) # | Thomas Scientific | KIK 949975 |
| Ethanol, Absolute (200 Proof) # | Sigma | E7023-500ML |
| SPRIselect Reagent Kit (contains SPRI beads) ∗ | Beckman Coulter | B23318 |
| Glycerin (glycerol), 50% (v/v) Aqueous Solution∗ | RICCA Chemical Company | 3290-32 |
| Qiagen Buffer EB∗ | QIAGEN | 19086 |
| Low TE Buffer∗ | Thermo Fisher Scientific | 12090-015 |
| Other | ||
| MasterCycler Pro Thermal Cycler# | Eppendorf | North America 950030010 International 6321 000.019 |
| Vortex Mixer# | VWR | 10153-838 |
| Fisherbrand™ motorized tissue grinder∗ | Thermo Fisher Scientific | 12-1413-61 |
| Fisherbrand™ RNase-Free Disposable Pellet Pestles∗ | Thermo Fisher Scientific | 12-141-364 |
| Divided Polystyrene Reservoirs# | VWR | 41428-958 |
| Tips∗ | Rainin | 30389240 (200 μL); 30389213 (1 mL); 30389226 (20 μL) |
| TempAssure PCR 8-tube strip∗ | USA Scientific | 1402-4700 |
| DNA LoBind Tubes, 1.5 mL# | Eppendorf | 022431021 |
| DNA LoBind Tubes, 2.0 mL# | Eppendorf | 022431048 |
| Mini Centrifuge# | Thermo Fisher Scientific | C1012 |
| Eppendorf ThermoMixer C# | Eppendorf | 5382000023/2231000574 |
| Drierite with indicator, 8 mesh# | Thermo Fisher Scientific (Acros Organics) | 21909-0020 |
| Pre-Separation Filters (70 μm) # | Miltenyi Biotec | 130-095-823 |
| Flowmi® Cell Strainers (40 μm) # | Sigma | H13680-0040 |
| 4200 TapeStation∗ | Agilent | G2991AA |
| High Sensitivity D1000 ScreenTape∗ | Agilent | 5067-5584 |
| High Sensitivity D1000 Reagents∗ | Agilent | 5067-5585 |
| 10× Vortex Adapter∗ | 10× Genomics | 120251(orderable), 330002 (Item) |
| Chromium Next GEM Secondary Holder∗ | 10× Genomics | 1000195(orderable), 3000332 (Item) |
| 10× Magnetic Separator∗ | 10× Genomics | 120250 (orderable), 230003 (Item) |
| NovaSeq6000# | Illumina | N/A |
| Qubit™ 4 Fluorometer∗ | Thermo Fisher Scientific | Q33238 |
| Qubit™ 1× dsDNA HS Assay Kit∗ | Thermo Fisher Scientific | Q33231 |
| Countess™ 3 FL Automated Cell Counter# | Thermo Fisher Scientific | AMQAF2000 |
| DAPI# | Thermo Fisher Scientific | R37606 |
| Countess™ Cell Counting Chamber Slides# | Thermo Fisher Scientific | C10283/C10228 |
| Biological samples | ||
| Adult postmortem human brain Age range: 74–90+ Sex: Male and Female |
UCI MIND’s Alzheimer’s Disease Research Center (ADRC) tissue repository | N/A |
| Deposited data | ||
| snATAC-seq data (postmortem frozen human brain tissue) | Synapse | Synapse ID: syn22079621 |
| snRNA-seq data (postmortem frozen human brain tissue) | Synapse | Synapse ID: syn22079621 |
| Software and algorithms | ||
| cellranger-atac | 10× Genomics | https://support.10×genomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac |
| R Version 4.1.1 | R Project | https://www.r-project.org |
| ArchR | (Granja et al., 2021) | https://www.archrproject.com/index.html |
| Signac | (Stuart et al., 2021) | https://satijalab.org/signac/index.html |
| Seurat | (Ntranos et al., 2019) | https://satijalab.org/seurat/ |
| Monocle3 | (Cao et al., 2019) | https://cole-trapnell-lab.github.io/monocle3/ |
| Cicero | (Pliner et al., 2018) | https://cole-trapnell-lab.github.io/cicero-release/ |
| GREAT | (McLean et al., 2010) | http://great.stanford.edu/public/html/ |
| ArchRtoSignac | Current Manuscript | https://github.com/swaruplabUCI/ArchRtoSignac/ DOI: 10.5281/zenodo.6612020 |
∗Critical Reagents/Instruments/Plasticwares/others.
#These are the Reagents/Instruments/Plasticwares that we used, although we can only speculate, we do not expect the use of alternative (compatible) reagents/instruments/ plasticwares to influence the efficiency of the assay. Please refer to Chromium Next GEM Single Cell ATAC Reagent Kits v1/v1.1 user manual for more information about alternatives.