KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse anti-CD83 | Bio-rad | Cat# MCA1582; RRID: AB_321773 |
| Mouse anti-CD83 | BioLegend | Cat# 305302; RRID: AB_314510 |
| Sheep anti-GFAP | R&D Systems | Cat# AF2594; RRID: AB_2109656 |
| Rabbit anti-IBA1 | WAKO | Cat# 019-19741; RRID: AB_839504 |
| Goat anti-OLIG2 | R&D Systems | Cat# AF2418; RRID: AB_2157554 |
| Rabbit anti-S100B | Sigma | Cat# S2644; RRID: AB_477501 |
| Goat anti-SOX2 | Santa Cruz | Cat# sc-17320; RRID: AB_2286684 |
| Goat anti-SOX2 | R&D Systems | Cat# AF2018; RRID: AB_355110 |
| Mouse anti-SOX2 | Abcam | Cat# ab79351; RRID: AB_10710406 |
| Rabbit anti-SOX6 | Millipore | Cat# AB5805; RRID: AB_2302618 |
| Donkey anti-goat secondary antibody, Cyanine 2 | Jackson ImmunoResearch | Cat# 705-225-147; RRID: AB_2307341 |
| Donkey anti-mouse secondary antibody, Cyanine 2 | Jackson ImmunoResearch | Cat# 715-225-151; RRID: AB_2340827 |
| Donkey anti-rabbit secondary antibody, Cyanine 2 | Jackson ImmunoResearch | Cat# 711-225-152; RRID: AB_2340612 |
| Donkey anti-sheep secondary antibody, Cyanine 2 | Jackson ImmunoResearch | 713-225-147; RRID: AB_2340735 |
| Donkey anti-goat secondary antibody, Cyanine 3 | Jackson ImmunoResearch | Cat# 705-165-147; RRID: AB_2307351 |
| Donkey anti-mouse secondary antibody, Cyanine 3 | Jackson ImmunoResearch | Cat# 715-165-151; RRID: AB_2315777 |
| Donkey anti-rabbit secondary antibody, Cyanine 3 | Jackson ImmunoResearch | Cat# 711-165-152; RRID: AB_2307443 |
| Biological samples | ||
| Human post-mortem hippocampal specimens | Children’s Hospital of Philadelphia; Johns Hopkins University Pathology Archive; Lieber Institute for Brain Development; Multiple repositories from the NIH NeuroBioBank | Full list in Table S1 |
| Chemicals, peptides, and recombinant proteins | ||
| Bovine serum albumin (BSA) | Life Technologies | Cat# 37525 |
| DAKO target retrieval solution (10X) | DAKO | Cat# S1699 |
| DAPI | Thermo Fisher Scientific | Cat# D1306; RRID: AB_2629482 |
| DL-Dithiothreitol (DTT) | Sigma | Cat# D0632 |
| dNTP | Thermo Fisher | Cat# R0192 |
| Donkey serum | Millipore | Cat# S30 |
| EDTA | cellgro | Cat# 46034Cl |
| EDTA-free protease inhibitor | Roche | Cat# 11836170001 |
| EvaGreen dye, 20X in Water | Biotium | Cat# 31000 |
| Ficoll solution, type 400 | Sigma | Cat# F5415-25ML |
| IGEPAL-630 | Sigma-Aldrich | Cat# I8896-50ML |
| Maxima H Minus Reverse Transcriptase | Fisher Scientific | Cat# EP0753 |
| MgCl2 | Thermo Fisher Scientific | Cat# AM9530G |
| Myelin Removal Beads II | Miltenyi Biotec | Cat# 130-096-733 |
| NaCl | Ambion | Cat# AM9760G |
| NEBuffer 3.1 | New England Biolabs | Cat# B7203s |
| Paraformaldehyde (PFA), 16%, methanol-free | Fisher Scientific | Cat# 50-980-487 |
| Phosphate-Buffered Saline (PBS) | Corning | Cat# 21-040 |
| PMSF protease inhibitor | Thermo Fisher | Cat# 36978 |
| Proteinase K Solution (20 mg/mL) | Thermo Fisher | Cat# AM2546 |
| RNase Inhibitor | Enzymatics | Cat# Y924L |
| SDS | Thermo Fisher | Cat# 15553027 |
| Sodium azide | Sigma-Aldrich | Cat# S2002 |
| Spermidine | Sigma-Aldrich | Cat# S0266-1G |
| Spermine | Sigma-Aldrich | Cat# S4264-1G |
| SPRIselect Beads | BECKMAN COULTER | Cat# B23318 |
| Sucrose | Sigma-Aldrich | Cat# S5016-500G |
| Superase-In RNase Inhibitor | Thermo Fisher | Cat# AM2694 |
| T4 DNA Ligase | New England Biolabs | Cat# M0202S |
| Tricine-KOH | Sigma-Aldrich | Cat# T5816-100G |
| Tris-HCl, pH8.0 | Ambion | Cat# AM9855G |
| Triton X-100 | Sigma-Aldrich | Cat# T9284 |
| Tween-20 | Thermo Fisher | Cat# 85113 |
| Xylene | Fisher Scientific | Cat# X5-1 |
| Critical Commercial Assays | ||
| Agilent High Sensitivity DNA Kit | Aligent | Cat# 5067-4626 |
| Dynabeads™ MyOne™ Streptavidin C1 Kit | Thermo Fisher | Cat# 65001 |
| Fuchs-Rosenthal hemocytometer | Incyto | Cat# DHCF015 |
| Kapa HiFi HotStart Master Mix | KAPA Biosystems | Cat# KK2601 |
| NextSeq 500/550 High Output v2.5 kit (150 cycles) | Illumina | Cat# 20024907 |
| Nextera XT DNA Library Preparation Kit | Illumina | Cat# FC-131-1024 |
| Qubit dsDNA HS Assay Kit | Thermo Fisher | Cat# Q32854 |
| TrueBlack Lipofuscin Autofluorescence Quencher | Biotium | Cat# 23007 |
| Oligonucleotides | ||
| Split barcode primer: Round 1/2/3 | IDT | (Rosenberg et al., 2018) |
| Deposited data | ||
| Human hippocampus snRNA-seq data | This paper | GSE185553, GSE198323 and GSE199243 |
| Human anterior cingulate cortex (ACC) and prefrontal cortex (PFC) snRNA-seq data (controls) | (Velmeshev et al., 2019) | PRJNA434002 |
| Human cerebellum, frontal cortex and visual cortex snRNA-seq data | (Lake et al., 2018) | GSE97930 |
| Human motor cortex snRNA-seq data (controls) | (Schirmer et al., 2019) | PRJNA544731 |
| Human white matter snRNA-seq data (controls) | (Jakel et al., 2019) | GSE118257 |
| Sliced human cortical organoid snRNA-seq data | (Qian et al., 2020) | GSE137941 |
| Sliced human brain organoid scRNA-seq data | (Szebenyi et al., 2021) | GSE180122 |
| iPSC-derived microglia cells scRNA-seq data | (Popova et al., 2021) | GSE180945 |
| iPSC-derived microglia cells scRNA-seq data | (Svoboda et al., 2019) | GSE139193 |
| iPSC-derived oligodendrocyte scRNA-seq data | (Chamling et al., 2021) | GSE146373 |
| iPSC-derived oligodendrocyte scRNA-seq data | (Marton et al., 2019) | GSE115011 |
| Software and algorithms | ||
| Adobe Illustrator CS6 | Adobe | https://www.adobe.com/products/illustrator.html; RRID: SCR_010279 |
| Adobe Photoshop CS6 | Adobe | https://www.adobe.com/products/photoshop.html; RRID:SCR_014199 |
| Bamtools (v2.3.0) | NA | https://bioinformatics.readthedocs.io/en/latest/bamtools/; RRID: SCR_015987 |
| bcl2fastq (v2.17.1) | Illumina | https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html; RRID: SCR_015058 |
| clusterProfiler (v4) | (Wu et al., 2021) | https://github.com/YuLab-SMU/clusterProfiler/; RRID: SCR_016884 |
| DAVID Knowledge Base (v2021q4) | https://david-d.ncifcrf.gov; RRID:SCR_001881 | |
| Drop-seq tools (v1.13) | (Macosko et al., 2015) | http://mccarrolllab.org/dropseq/; RRID: SCR_018142 |
| GeneOverlap | (Shen, 2021) | https://bioconductor.org/packages/release/bioc/html/GeneOverlap.html; RRID:SCR_018419 |
| Imaris 9.0 | Bit Plane | http://www.bitplane.com/imaris/imaris/; RRID: SCR_007370 |
| JAVA (v 1.8.0) | JAVA | https://www.java.com/en/download/ |
| Microsoft Excel | Microsoft | https://www.microsoft.com/en-us/p/excel/cfq7ttc0k7dx?activetab=pivot%3aoverviewtab; RRID: SCR_016137 |
| PicardTools (v2.13.2) | Broad Institute | http://broadinstitute.github.io/picard/; RRID: SCR_006525 |
| R (v4.0.4) | R | https://cran.r-project.org/; RRID: SCR_001905 |
| R Studio | RStudio | https://rstudio.com/; RRID: SCR_000432 |
| randomForest (v4.6.14) | (Breiman, 2001) | https://cran.r-project.org/web/packages/randomForest/index.html; RRID: SCR_015718 |
| Samtools (v1.1) | NA | http://www.htslib.org/; RRID:SCR_005227 |
| scDbiFinder (v1.4.0) | (Germain et al., 2021) | https://bioconductor.org/packages/release/bioc/html/scDblFinder.html |
| sctransform (v0.3) | (Hafemeister and Satija, 2019) | https://github.com/ChristophH/sctransform |
| Seurat (v 4.0.0) | (Hao et al., 2021) | https://satijalab.org/seurat/; RRID: SCR_007322 |
| STAR (v2.5.2a) | (Dobin et al., 2013) | https://github.com/alexdobin/STAR; RRID: SCR_015899 |
| UMAP | R package | https://umap-learn.readthedocs.io/en/latest/; RRID:SCR_018217 |
| Zen 2 | Carl Zeiss | https://www.zeiss.com; RRID: SCR_013672 |
| Other | ||
| 40-μm cell strainer | Fisher Scientific | 22-363-547 |
| Bioanalyzer 2100 | Aligent | G2939BA |
| Confocal microscope | Carl Zeiss | Zeiss LSM 800 |
| Dounce homogenizer | Fisher Scientific | 8853000002 |
| Frozen sliding microtome | Leica | Cat# SM2010R |
| Illumina NextSeq 550 sequencer | Illumina | |
| Qubit Fluorometer | Thermo Fisher Scientific | Q33238 |
| T100 Thermal Cycler | Bio-rad | 1861096EDU |