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 |