| Antibodies |
| Alexa Fluor 488-conjugated anti-NeuN-AF488 |
Millipore Sigma |
MAB377X |
| Biological samples |
| Human postmortem brain tissue |
Lieber Institute for Brain Development (see Table S1) |
NA |
| Chemicals, peptides, and recombinant proteins |
| Nuclei EZ Lysis Buffer |
Millipore Sigma |
NUC101 |
| Optimal Temperature Compound |
TissueTek Sakura |
4583 |
| 10% neutral buffered formalin solution |
Sigma-Aldrich |
HT501128 |
| Saline sodium citrate |
Quality Biological |
351–003-101 |
| TSA Buffer |
Advanced Cell Diagnostics [ACD] |
322809 |
| Fluoromount-G |
ThermoFisher |
00-4958-02 |
| Critical commercial assays |
| RNAScope Multiplex Fluorescent Reagent Kit v2 |
Advanced Cell Diagnostics [ACD] |
323100 |
| RNAScope 4-Plex Ancillary Kit |
Advanced Cell Diagnostics [ACD] |
323120 |
|
MBP RNAScope probe |
Advanced Cell Diagnostics [ACD] |
411051 & 411051-C4 |
|
ELAVL2 RNAScope probe |
Advanced Cell Diagnostics [ACD] |
540301-C3 |
|
PPP1R1B RNAScope probe |
Advanced Cell Diagnostics [ACD] |
477021 |
|
TRPC4 RNAScope probe |
Advanced Cell Diagnostics [ACD] |
1226941-C2 |
|
GAD1 RNAScope probe |
Advanced Cell Diagnostics [ACD] |
404031-C3 |
|
OPRM1 RNAScope probe |
Advanced Cell Diagnostics [ACD] |
410681-C4 |
|
FREM2 RNAScope probe |
Advanced Cell Diagnostics [ACD] |
482841 |
| Opal 520 fluorescent dye |
Akoya Biosciences [AB] |
FP1487001KT |
| Opal 570 fluorescent dye |
Akoya Biosciences [AB] |
FP1488001KT |
| Opal 620 fluorescent dye |
Akoya Biosciences [AB] |
FP1495001KT |
| Opal 690 fluorescent dye |
Akoya Biosciences [AB] |
FP1497001KT |
| Chromium NextGEM Single Cell 3’ Reagent Kit (v3.1) Dual-Index |
10x Genomics |
1000268 |
| Dual-Index Kit TT Set A |
10x Genomics |
1000215 |
| Deposited data |
| Raw Sequence Reads |
This manuscript |
SRA project accession: PRJNA1093410 |
| SingleCellExperiment Object (link: jhpce#ls_molecular-profiling_sce) |
This manuscript |
https://research.libd.org/globus/
|
| Software and algorithms |
| CellRanger v7.2.0 |
10X Genomics |
https://www.10xgenomics.com/support/software/cell-ranger/7.2
|
| R v4.4.0 |
R core team |
https://www.r-project.org/
|
| Bioconductor suite of single-cell analytical packages v3.19 |
Gentleman et al. 2004 [24] and Amezquita et al. 2020 [25] |
https://bioconductor.org/
|
| NIS-Elements |
v5.42.02 |
https://www.microscope.healthcare.nikon.com/products/software/nis-elements
|
| DeconvoBuddies |
V0.99.0 |
https://research.libd.org/DeconvoBuddies/index.html
|
| Other |
| Original code for analyses within this manuscript |
This manuscript |
https://zenodo.org/records/13799049 & https://github.com/LieberInstitute/ls_molecular-profiling
|
| Interactive web-based app |
This manuscript |
https://libd.shinyapps.io/LS_snRNAseq/
|
