KEY RESOURCES TABLE.
(Tran, Maynard, et al. 2021 submission)
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-NeuN (clone A60), Alexa Fluor 488-conjugated | MilliporeSigma | #MAB377X |
| Biological samples | ||
| Human postmortem brain tissue (NAc, AMY, sACC, DLPFC, HPC) | Lieber Institute for Brain Development; see Tables S1 and S2 | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Recombinant RNasin ribonuclease inhibitor | Promega | N2515 |
| 4’,6-diamidino-2-phenylindole, dihydrochloride (DAPI) | Invitrogen | D1306 |
| Propidium iodide solution (PI), 1mg/mL | Invitrogen | P3566 |
| Bovine serum albumin (BSA) | VWR | 102643-516 |
| 10% neutral buffered formalin | Sigma-Aldrich | HT501128 |
| Critical commercial assays | ||
| Nuclei EZ Prep (lysis buffer) | Sigma-Aldrich | NUC101-1KT |
| Chromium Single Cell 3’ GEM, Library & Gel Bead Kit, v3 | 10x Genomics | PN-1000075 |
| Chromium Single Cell B Chip Kit | 10x Genomics | PN-1000073 |
| RNAscope Multiplex Fluorescent Kit, v2 | ACD | 323100 |
| RNAscope 4-Plex Ancillary Kit | ACD | 323120 |
| Deposited data | ||
| Raw sequencing read data (FASTQ) for all n=24 samples reported in this paper | This paper | https://research.libd.org/globus/jhpce_tran2021/index.html |
| Processed data as ‘SingleCellExperiment’ R objects, for each region (NAc, AMY, sACC, DLPFC, HPC) | This paper | Linked from: https://github.com/LieberInstitute/10xPilot_snRNAseq-human#readme |
| Summary statistics from various Psychiatric Genomics Consortium GWAS | (Various author lists) | https://www.med.unc.edu/pgc/download-results/ |
| Summary statistics for substance use phenotypes GWAS | Liu, et al. 2019 | https://genome.psych.umn.edu/index.php/GSCAN |
| Software and algorithms | ||
| Cell Ranger, v3.0 | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/3.0/installation |
| R, v4.0.4 | R Core Team | https://www.r-project.org/ |
| Orchestrating single-cell analysis with Bioconductor (v3.12 methods/R packages) | Amezquita, et al. 2019 | https://doi.org/10.1038/s41592-019-0654-x |
| MAGMA, v1.08 | De Leeuw, et al. 2015 | https://ctg.cncr.nl/software/magma |
| Other | ||
| Code for analyses in the present study | This paper | https://doi.org/10.5281/zenodo.5149046 |