KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit anti-MAP2 polyclonal | MilliporeSigma | Cat#AB5622 |
| Mouse anti-NeuN | MilliporeSigma | Cat#MAB377 |
| Mouse anti-phospho-Tau Ser202, Thr205 monoclonal (AT8) | ThermoFisher | Cat#MN1020 |
| Rabbit polyclonal anti oligomeric tau (T22) | MilliporeSigma | Cat#ABN454 |
| Recombinant rabbit anti-phospho-Tau (Ser396) monoclonal [EPR2731] | Abcam | Cat#ab109390 |
| Phospho-Tau (Thr205) Polyclonal | ThermoFisher | Cat#44-738G |
| Recombinant anti-SQSTM1/p62 [EPR4844] | Abcam | Cat#ab109012 |
| HRP Anti-beta Actin [AC-15] | Abcam | Cat# ab49900 |
| Lamin B1 (D4Q4Z) Rabbit monoclonal | Cell Signaling Technology | Cat#12586 |
| Histone H3 C-terminal | EpiCypher | Cat#13-0001 |
| Biological Samples | ||
| Human postmortem brain tissue | Table S1 | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| RNAscope Probe SLC17A7 | ACD Bio | Cat#415611 |
| RNAscope Probe GAD1 | ACD Bio | Cat#404031 |
| RNAscope Probe CUX2 | ACD Bio | Cat#425581 |
| RNAscope Probe LAMP5 | ACD Bio | Cat#487691 |
| RNAscope Probe COL5A2 | ACD Bio | Cat#510911 |
| RNAscope Probe RORB | ACD Bio | Cat#446061 |
| RNAscope Probe GAL | ACD Bio | Cat#317631 |
| RNAscope Probe GABRG1 | ACD Bio | Cat#485931 |
| RNAscope Probe RPRM | ACD Bio | Cat#565701 |
| RNAscope Probe PCP4 | ACD Bio | Cat#446111 |
| RNAscope Probe ROBO3 | ACD Bio | Cat#483191 |
| RNAscope Probe NR4A2 | ACD Bio | Cat#582621 |
| RNAscope Probe NTNG2 | ACD Bio | Cat#551651 |
| RNAscope Probe SNAP25 | ACD Bio | Cat#518851 |
| RNAscope Probe GABRA1 | ACD Bio | Cat#472141 |
| RNAscope Probe GRIN2B | ACD Bio | Cat#485851 |
| RNAscope Probe SYT1 | ACD Bio | Cat#525791 |
| RNAscope Probe AFT4 | ACD Bio | Cat#405741 |
| Critical Commercial Assays | ||
| Chromium Single Cell 3’ v2 Reagent Kit | 10x Genomics | PN-120237 |
| RNAscope Multiplex Fluorescent Reagent Kit v2 | ACD Bio | Cat#323120 |
| RNAscope 2.5 HD Duplex Assay | ACD Bio | Cat#322430 |
| Deposited Data | ||
| Raw and processed data | This paper | GSE129308 |
| Published dataset | Mathys et al., 2019 | https://www.synapse.org/#!Synapse:syn18485175 |
| Published dataset | Leng et al., 2021 | https://cellxgene.cziscience.com/collections/180bff9c-c8a5-4539-b13b-ddbc00d643e6 |
| Software and Algorithms | ||
| Seurat | Seurat v2.4, v3 and v4 | https://satijalab.org/seurat/ |
| Fiji/ImageJ | Fiji v.2.3.1 | RRID:SCR_002285 |
| Adobe Illustrator CC | Adobe Systems | RRID:SCR_010279 |
| SynGO | SynGO consortium | https://www.syngoportal.org/ |
| g:Profiler | g:Profiler version Ensembl 97, Ensembl Genomes 44 | https://biit.cs.ut.ee/gprofiler/gost |
| Cytoscape | Cytoscape v3.8.2 | RRID:SCR_003032 |
| Stereo Investigator | MBF Bioscience v.2018 | RRID:SCR_002526 |
| Cell Ranger | 10x Genomics | RRID:SCR_017344 |