Appendix 1—key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Antibody | GFP (chicken polyclonal) |
Aves Lab | Cat# GFP-1020 | IF (1:1000) |
| Antibody | CD31 (mouse monoclonal) |
Abcam | Cat# ab9498 | IF (1:300) |
| Antibody | PDGFRβ (goat polyclonal) |
R&D | Cat# AF1042 | IF (1:200) |
| Antibody | αSMA (rabbit monoclonal) |
Abcam | Cat# ab124964 | IF (1:500) |
| Antibody | DCX (goat polyclonal) |
Santa Cruz | Cat# sc-8066 | IF (1:200) |
| Antibody | CLDN5 (mouse monoclonal) |
Abcam | Cat# ab131259 | IF (1:500) |
| Antibody | IBA1 (rabbit monoclonal) |
Wako | Cat# 019-19741 | IF (1:500) |
| Antibody | PAX6 (sheep polyclonal) |
R&D | Cat# AF8150 | IF (1:500) |
| Antibody | p-VIM (mouse monoclonal) |
MBL | Cat# D076-3 | IF (1:1000) |
| Antibody | DLL4 (rabbit polyclonal) |
Abcam | Cat# ab7280 | IF (1:500) |
| Antibody | EPHB4 (rabbit monoclonal) |
Cell Signaling | Cat# 14960 | IF (1:500) |
| Antibody | KI67 (mouse monoclonal) |
BD | Cat# 550609 | IF (1:1000) |
| Antibody | TBR2 (mouse monoclonal) |
R&D | Cat# AF6166 | IF (1:400) |
| Antibody | TUJ1 (chicken polyclonal) |
Abcam | Cat# ab41489 | IF (1:1000) |
| Antibody | TBR1 (rabbit polyclonal) |
Abcam | Cat# ab31940 | IF (1:500) |
| Antibody | CTIP2 (rat monoclonal) |
Abcam | Cat# ab18465 | IF (1:500) |
| Antibody | SATB2 (rabbit polyclonal) |
Abcam | Cat# ab69995 | IF (1:400) |
| Antibody | PSD95 (rabbit monoclonal) |
Cell Signaling | Cat# 3450S | IF (1:500) |
| Antibody | ZO-1 (rabbit monoclonal) |
Abcam | Cat# ab221547 | IF (1:500) |
| Antibody | GLUT1 (rabbit monoclonal) |
Abcam | Cat# ab115730 | IF (1:500) |
| Antibody | p-Glycoprotein (rabbit monoclonal) |
Abcam | Cat# ab170904 | IF (1:500) |
| Antibody | Cleaved-CASPASE3 (rabbit polyclonal) |
Cell Signaling | Cat# 9661L | IF (1:500) |
| Antibody | TMEM119 (rabbit polyclonal) |
Abcam | Cat# ab185333 | IF (1:500) |
| Antibody | TREM2 (rabbit monoclonal) |
Abcam | Cat# ab209814 | IF (1:500) |
| Antibody | Human-Nuclei (mouse monoclonal) |
Millipore | Cat# MAB1281 | IF (1:500) |
| Antibody | Anti-Hu CD31 Alexa 647 WM59 50Tst | BD | Cat# 561654 | Flow cytometry (1:1000) |
| Peptide, recombinant protein | Hu Recom bFGF | STEMCELL | Cat# 78003 | |
| Peptide, recombinant protein | Hu Recom VEGF | STEMCELL | Cat# 78073 | |
| Peptide, recombinant protein | Hu Recom BMP4 | R&D | Cat# 314BP | |
| Peptide, recombinant protein | Insulin | Sigma-Aldrich | Cat# I9278 | |
| Peptide, recombinant protein | Human Dil-acetylated low-density lipoprotein | Yeasen | Cat# 20606ES76 | |
| Chemical compound, drug | Y27632 | STEMCELL | Cat# 72304 | |
| Chemical compound, drug | Dorsomorphine | Tocris | Cat# 3093/10 | |
| Chemical compound, drug | A83-01 | Tocris | Cat# 2939/10 | |
| Chemical compound, drug | CHIR99021 | Selleck | Cat# S1263 | |
| Chemical compound, drug | LDN-193189 2HCL | Selleck | Cat# S7507 | |
| Chemical compound, drug | SB431542 | Selleck | Cat# S1067 | |
| Chemical compound, drug | TTX | Tocris | Cat# 1069 | |
| Chemical compound, drug | DNQX | Tocris | Cat# 0189 | |
| Chemical compound, drug | DL-AP5 | Tocris | Cat# 3693 | |
| Chemical compound, drug | Trypsin inhibitor | Sigma-Aldrich | Cat# T6522 | |
| Chemical compound, drug | PLX5622 | MCE | Cat# HY-11415 | |
| Chemical compound, drug | LPS | MCE | Cat# HY-D1056 | |
| Commercial assay, kit | SYBR Green PCR mix | Bimake | Cat# B21702 | |
| Commercial assay, kit | RNeasy Plus Micro Kit | QIAGEN | Cat# 74034 | |
| Commercial assay, kit | GoScript Reverse Transcription Kit | Promega | Cat# A5001 | |
| Commercial assay, kit | Pon812 812 kit | SPI | Cat# GS02660 | |
| Commercial assay, kit | Toluidine blue | Sinopharm | Cat# XW65860453 | |
| Commercial assay, kit | Uranyl acetate | SPI | Cat# GS02624 | |
| Commercial assay, kit | Lead citrate | SPI | Cat# GP19314 | |
| Commercial assay, kit | Single Cell Reagent Kits | 10x Genomics | N/A | |
| Software, algorithm | Cellranger | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome | |
| Software, algorithm | Seurat (v3) | Macosko et al., 2015 | https://satijalab.org/seurat/ | |
| Software, algorithm | R (v3.5.2) | N/A | https://www.r-project.org/ | |
| Software, algorithm | clusterProfiler (v3.10.1) | http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html | ||
| Software, algorithm | Limma (v3.38.3) | http://bioconductor.org/packages/release/bioc/html/limma.html | ||
| Software, algorithm | Monocle (v2.10.1) | http://cole-trapnell-lab.github.io/monocle-release/ | An analysis toolkit for single-cell RNA-seq. | |
| Software, algorithms | Fiji | N/A | https://fiji.sc | |
| Software, algorithm | Angiotool (v 0.6a) | Zudaire et al., 2011 | http://angiotool.nci.nih.gov | |
| Software, algorithm | Reference Transcriptome for GRCh38 (v1.2.0) | N/A | https://genome.ucsc.edu/ | |
| Other | Heparin | Sigma-Aldrich | Cat# H3393 | Section ‘Generation of human brain organoid’ |
| Other | Lipidure | NOF CORPORATION | Cat# CM5206 | Section ‘Generation of human brain organoid’ |
| Other | Antibiotic-Antimycotic | Gibco | Cat# 15240096 | Section ‘Generation of human brain organoid’ |
| Other | Matrigel hESC-Qualified Matrix | BD-Biocoat | Cat# 354277 | Section ‘hESCs culture’ |
| Other | Matrigel growth factor reduced (GFR) basement membrane matrix | BD-Biocoat | Cat# 354230 | Section ‘Generation of human brain organoid’ |
| Other | STEMdiff APEL2 Medium | STEMCELL | Cat# 05270 | Section ‘Generation of human vessel organoid’ |
| Other | Endothelial cell growth medium MV2 | PromoCell | Cat# C-22022 | Section ‘Generation of human vessel organoid’ |
| Other | mTeSR1 | STEMCELL | Cat# 85850 | Section ‘hESCs culture’ |
| Other | ReLeSR | STEMCELL | Cat# 05872 | Section ‘hESCs culture’ |
| Other | Accutase | STEMCELL | Cat# 07920 | Section ‘Generation of human brain organoid’ |
| Other | O.C.T | Sakura | Cat# 4583 | Section ‘Immunofluorescence’ |
| Other | BSA | Sigma-Aldrich | Cat# V900933 | Section ‘Immunofluorescence’ |
| Other | TritonX-1000 | Sigma-Aldrich | Cat# T8787 | Section ‘Immunofluorescence’ |
| Other | Neurobasal | Life/Invitrogen | Cat# 21103049 | Section ‘Generation of human brain organoid’ |
| Other | N2 supplement | Life/Invitrogen | Cat# 17502048 | Section ‘Generation of human brain organoid’ |
| Other | B27 supplement without vitamin A | Life/Invitrogen | Cat# 12587010 | Section ‘Generation of human brain organoid’ |
| Other | B27 supplement | Life/Invitrogen | Cat# 17504044 | Section ‘Generation of human brain organoid’ |
| Other | DPBS | Life/Invitrogen | Cat# 14190144 | Section ‘hESCs culture’ |
| Other | HBSS | Life/Invitrogen | Cat# 14175069 | Section ‘Single-cell dissociation and 10x Genomics chromium library construction’ |
| Other | HEPES | Sigma-Aldrich | Cat# H4034 | Section ‘Single-cell dissociation and 10x genomics chromium library construction’ |
| Other | DNase I | Roche | Cat# 10104159001 | Section ‘Single-cell dissociation and 10x Genomics chromium library construction’ |
| Other | Knockout Serum Replacer | Gibco | Cat# 10828028 | Section ‘Generation of human brain organoid’ |
| Other | MEM-NEAA | Gibco | Cat# 11140050 | Section ‘Generation of human brain organoid’ |
| Other | GlutaMAX | Gibco | Cat# 35050061 | Section ‘Generation of human brain organoid’ |
| Other | β-Mercaptoethanol | Sigma-Aldrich | Cat# M3148 | Section ‘Generation of human brain organoid’ |
| Other | Bovine pancreatic trypsin | Sigma-Aldrich | Cat# 6502 | Section ‘Single-cell dissociation and 10x Genomics chromium library construction’ |
| Other | Leibovitz L-15 medium | Thermo | Cat# 11415064 | Section ‘Single-cell dissociation and 10x Genomics chromium library construction’ |
| Other | DMEM/F12 | Life/Invitrogen | Cat# 10565018 | Section ‘hESCs culture’ |