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. Author manuscript; available in PMC: 2023 Sep 21.
Published in final edited form as: Neuron. 2022 Jul 25;110(18):2929–2948.e8. doi: 10.1016/j.neuron.2022.06.021

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