Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference |
Identifiers | Additional information |
|---|---|---|---|---|
| Strains, strain backgrounds (mice) | Cdh5(PAC)-Cre-ERT2, C57BL/6 background | Wang et al., 2010 | ||
| Strains, strain backgrounds (mice) | Cdh5(PAC)-Cre- ERT2/Ccm3f/f, C57BL/6 background | Bravi et al., 2015 | ||
| Strains, strain backgrounds (mice) | Cldn5(BAC)-GFP (Tg(Cldn5-GFP)Cbet/U), C57BL/6 background | Honkura et al., 2018 | ||
| Strains, strain backgrounds (mice) | Cdh5(PAC)-Cre-ERT2/Ccm3f/f/Cldn5(BAC)-GFP, C57BL/6 background | This paper | ||
| Antibody | Anti-CD93 (sheep polyclonal) | R and D | AF1696, RRID:AB_354937 | IF (1:500) |
| Antibody | Anti-Erg (rabbit monoclonal) | Abcam | Ab92513, RRID:AB_2630401 | IF (1:400) |
| Antibody | Anti-Ki67 (rat monoclonal) | Invitrogen | 14-5698-82, RRID:AB_10854564 | IF (1:200) |
| Antibody | Anti-Podocalyxin (goat polyclonal) | R and D | AF1556, RRID:AB_354858 | IF (1:400) |
| Antibody | Anti-CoupTFII (rabbit polyclonal) | LSBio | LS-C356225 | IF (1:200) |
| Antibody | Anti-PECAM-1 (rat monoclonal) | BD | 55369, RRID:AB_394815 | IF (1:200) |
| Antibody | Anti-PECAM-1 (armenian hamster monoclonal) | Millipore | MAB1398z, RRID:AB_94207 | IF (1:500) |
| Antibody | Anti-Claudin-5 (mouse monoclonal, Alexa fluor 488-conjugated) | Invitrogen | 352588, RRID:AB_2532189 | IF (1:200) |
| Antibody | Anti-VE-cadherin (rat monoclonal) | BD | 550548, RRID:AB_2244723 | IF (1:200) |
| Antibody | Anti-Cingulin (rabbit polyclonal) | Invitrogen | 36–4401 | IF (1:500) |
| Antibody | Alexa Fluor 488, 555 and 647 donkey secondary antibodies | Jackson laboratories | IF (1:400) | |
| Antibody | Alexa Fluor 488 conjugated donkey anti-mouse | Jackson laboratories | IF (1:400) | |
| Antibody | Anti-uPAR antibody | Tjwa et al., 2009 | IF (1:200) | |
| Commercial assays or kits | 3-Plex positive controls | ACD | #320881 | for detecting Polr2a, PPIB, UBC mRNA |
| Commercial assays or kits | 3-Plex negative controls | ACD | #320871 | for detecting DapB mRNA of Bacillus subtilis |
| Commercial assays or kits | Multiplex fluorescent Reagent Kit v2 | ACD | 323100 | |
| Commercial assays or kits |
Cldn5 | ACD | 491611-C2 | |
| Commercial assays or kits | Bst1 | ACD | 559841-C3 | |
| Commercial assays or kits | CD45 MicroBeads | Miltenyi Biotech | 130-052-301 | |
| Commercial assays or kits | CD31 MicroBeads | Miltenyi Biotech | 130-097-418, RRID:AB_2814657 | |
| Commercial assays or kits | Adult Brain Dissociation kits | Miltenyi Biotech | 130-107-677 | |
| Commercial assays or kits | Single Cell 3’ Reagent kits v2 | 10 × genomics | PN-120237 | |
| Instruments | GentleMACS Octo Dissociator | Miltenyi Biotech | 130-095-937 | |
| Instruments | Chromium controller | 10 × genomics | NA | |
| Instruments | NovaSeq 6000 system | Illumina | RRID:SCR_016387 | |
| Instruments | Vibratome | Leica | VT1200s, RRID:SCR_018453 | |
| Instruments | Sp8 confocal microscope | Leica | ||
| Instruments | Cryostat | Thermo Scientific | CryoStar NX50 | |
| Instruments | High Sensitivity RNA ScreenTape | Agilent | ||
| Others | Visium Spatial Gene Expression slides | 10 × genomics | PN-2000233 | |
| Others | Visium Tissue Optimization Slides and reagents | 10 × genomics | PN-1000193 | |
| Software, algorithms | Fiji | open source, http://fiji.sc/ | RRID:SCR_002285 | |
| Software, algorithms | Cell Ranger | 10 × genomics | v2.1.0, RRID:SCR_017344 | |
| Software, algorithms | R package Seurat | Butler et al., 2018; Stuart et al., 2019 | v3.1, RRID:SCR_016341 | |
| Software, algorithms | R package clustree | Zappia and Oshlack, 2018 | v0.4.2, RRID:SCR_016293 | |
| Software, algorithms | R package EnrichR | Chen et al., 2013; Kuleshov et al., 2016 | v2.1, RRID:SCR_001575 | https://amp.pharm.mssm.edu/Enrichr/ |
| Software, algorithms | GSEA | Liberzon et al., 2015; Subramanian et al., 2005 | v2.2.3, RRID:SCR_003199 | https://www.gsea-msigdb.org/gsea/msigdb/annotate.jsp |
| Software, algorithms | STREAM | Chen et al., 2019 | v0.4.1 | |
| Software, algorithms | Space Ranger | 10 × genomics | v1.0.0 | |
| Software, algorithms | Loupe cell browser | 10 × genomics | v4.0, RRID:SCR_018555 |