KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Olfm4 (D6Y5A) XP® Rabbit mAb (Mouse Specific) | Cell Signaling Technology | Cat#39141S; RRID: AB_2650511 |
| Mouse Reelin Antibody AF3820 | R&D systems | Cat#AF3820; RRID: AB_2253745 |
| Human LYVE-1 Antibody (goat) | R&D systems | Cat#AF2089; RRID: AB_355144 |
| Human/Mouse E-Cadherin Antibody | R&D systems | Cat#AF748; RRID: AB_355568 |
| E-Cadherin (24E10) Rabbit mAb #3195 | Cell Signaling Technology | Cat#3195S; RRID: AB_2291471 |
| Anti-Aldolase B Antibody | Abcam | Cat#ab75751; RRID: AB_2226682 |
| CD140a (PDGFRA) Monoclonal Antibody (APA5), APC, eBioscience™ | ThermoFisher | Cat#17-1401-81; RRID: AB_529482 |
| APC/Cyanine7 anti-mouse CD45 Antibody | Biolegend | Cat#103116; RRID: AB_312981 |
| LYVE1 Monoclonal Antibody (ALY7), eFluor 660, eBioscience™ | ThermoFisher | Cat#50-0443-82; RRID: AB_10597449 |
| LYVE1 Monoclonal Antibody (ALY7), eBioscience | ThermoFisher | Cat#14-0443-82; RRID: AB_1633414 |
| anti-mouse LYVE-1 | Angiobio | Cat#11-034; RRID: AB_2813732 |
| PE anti-mouse Podoplanin Antibody | Biolegend | Cat#127408; RRID: AB_2161928 |
| PerCP/Cyanine5.5 anti-mouse Podoplanin Antibody | Biolegend | Cat#127422; RRID: AB_2814016 |
| E-Cadherin (4A2) Mouse mAb #14472 | Cell Signaling Technology | Cat#14472S; RRID: AB_2728770 |
| Purified anti-mouse CD326 (Ep-CAM) Antibody | Biolegend | Cat#118202; RRID: AB_1089027 |
| FITC anti-mouse CD31 Antibody | Biolegend | Cat#102506; RRID: AB_312913 |
| PE/Cyanine7 anti-mouse CD326 (Ep-CAM) Antibody | Biolegend | Cat#118216; RRID: AB_1236471 |
| Anti-Prox1 Ab (rabbit, 100 ug) | Angiobio | Cat#11-002P |
| PE/Cyanine7 anti-mouse CD31 Antibody | Biolegend | Cat#102524; RRID: AB_10013720 |
| Endomucin Antibody (V.7C7): sc-65495 | SantaCruz | Cat#SC65495; RRID: AB_2100037 |
| Polyclonal Rabbit Anti-Human Lysozyme | Dako | Cat#EC 3.2.1.17; RRID: AB_2341231 |
| Anti-Reelin (CR-50) mAb (Monoclonal Antibody) | MBL International | Cat# D223-3; RRID: AB_843523 |
| TruStain FcX™ (anti-mouse CD16/32) Antibody | Biolegend | Cat#101320; RRID: AB_1574975 |
| Donkey anti-Sheep IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 | ThermoFisher | Cat#A-21448; RRID: AB_2535865 |
| APC anti-mouse CD170 (Siglec-F) Antibody | Biolegend | Cat#155508; RRID: AB_2750237 |
| Phospho-Dab1 (Tyr220) Antibody #3327 | Cell Signaling Technology | Cat#3327S; RRID: AB_2267690 |
| DAB1 Antibody (PA5-85453) | ThermoFisher | Cat#PA5-85453; RRID: AB_2792593 |
| Anti-GFP Polyclonal Chicken | Abcam | Cat#ab13970; RRID: AB_300798 |
| Guineapig anti Sox9 | Elaine Fuchs’ Lab | N/A |
| Recombinant Anti-SOX9 antibody [EPR14335-78] (ab185966) | Abcam | Cat#ab185966; RRID: AB_2728660 |
| Cleaved Caspase-3 (Asp175) (5A1E) Rabbit mAb #9664 | Cell Signaling Technology | Cat#9664; RRID: AB_2070042 |
| Anti-PECAM-1 Antibody, clone 2H8, Azide Free | MilliporeSigma | Cat#MAB1398Z; RRID: AB_94207 |
| Purified NA/LE Hamster Anti-Rat CD29 | BD bioscience | Cat#555002; RRID: AB_395636 |
| Purified Mouse Anti-CD29 | BD bioscience | Cat#610467; RRID: AB_2128060 |
| α-Smooth Muscle Actin (D4K9N) XP® | Cell Signaling Technology | Cat#19245; RRID: AB_2734735 |
| β-Actin (8H10D10) Mouse mAb #3700 | Cell Signaling Technology | Cat#3700S; RRID: AB_2242334 |
| Biological samples | ||
| Human organoids | Memorial Sloan Kettering Cancer Center | N/A |
| Human intestinal tissue | Jill Roberts Center for Inflammatory Bowel Disease | N/A |
| Mouse intestinal tissue from VE-Cadherin-CreERT2 Reelinflox/Δ mice and Reelinflox/flox mice | Gift from Guillermo Oliver | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Recombinant Mouse Reelin Protein | R&D Systems | Cat#3820-MR-025 |
| Recombinant Human R-Spondin 1 Protein | R&D Systems | Cat#4645-RS-250 |
| Recombinant Murine Noggin | Prepotech | Cat#250-38 |
| EGF Recombinant Mouse Protein | ThermoFisher | Cat#PMG8041 |
| Recombinant Murine Wnt-3a | Prepotech | Cat#315-20 |
| Recombinant Mouse LRPAP Protein, CF | R&D Systems | Cat#4480-LR-050 |
| N-Acetyl-L-cysteine | MilliporeSigma | Cat#A7250-50G |
| EDTA (0.5 M), pH 8.0, RNase-free | ThermoFisher | Cat#AM9260G |
| Gelatin-Based Coating Solution | Cell Biologics | Cat#6950 |
| Ethyl cinnamate | MilliporeSigma | Cat#112372-100G |
| L-Glutamine (200 mM) | ThermoFisher | Cat#25030081 |
| GlutaMAX™ Supplement | ThermoFisher | Cat#35050061 |
| TRIzol™ Reagent | ThermoFisher | Cat#15596026 |
| Diphtheria Toxin from Corynebacterium diphtheriae | MilliporeSigma | Cat#D0564 |
| Tamoxifen | MilliporeSigma | Cat#T5648 |
| Gibco™ B-27™ Supplement (50X), serum free | Fisher Scientific | Cat#17-504-044 |
| HEPES (1 M) | ThermoFisher | Cat#15630080 |
| PRIMOCIN | Fisher Scientific | Cat#NC9141851 |
| NORMOCIN | Fisher Scientific | Cat#NC9273499 |
| Gentle Cell Dissociation Reagent | Stem Cell Technology | Cat#100-0485 |
| Corning® Matrigel® Matrix for Organoid Culture, Phenol Red-free, LDEV-free | Corning | Cat#356231 |
| Cultrex UltiMatrix Reduced Growth Factor Basement Membrane Extract | R&D systems | Cat#BME001-10 |
| Gibco™ TrypLE™ Express Enzyme (1X), no phenol red | Fisher Scientific | Cat#12-604-021 |
| COMPLETE MOUSE ENDOTHELIAL CELL MEDIUM /W KIT | Cell Biologics | Cat# M1168 |
| Advanced DMEM/F-12 | Thermo Fisher | Cat#12634028 |
| Endothelial Cell Growth Medium MV 2 | PromoCell | Cat#C-22121 |
| ProLong™ Gold Antifade Mountant with DAPI | Thermo Fisher | Cat#P36935 |
| Normal Donkey Serum | JacksonImmunoResearch Lab | Cat#017-000-121 |
| RIPA Lysis and Extraction Buffer (Roche) | ThermoFisher | Cat#89901 |
| PhosSTOP™ (Roche) | MilliporeSigma | Cat#4906837001 |
| cOmplete™ Protease Inhibitor Cocktail (Roche) | MilliporeSigma | Cat#11836145001 |
| NuPAGE™ LDS Sample Buffer (4X) | ThermoFisher | Cat#NP0008 |
| NuPAGE™ Sample Reducing Agent (10X) | ThermoFisher | Cat#NP0009 |
| Precision Plus Protein™ Dual Color Standards | Biorad | Cat#1610374EDU |
| NuPAGE™ 4 to 12%, Bis-Tris, 1.0–1.5 mm | ThermoFisher | Cat#:NP0321BOX |
| NuPAGE™ MOPS SDS Running Buffer (20X) | ThermoFisher | Cat#NP0001 |
| NuPAGE™ Transfer Buffer (20X) | ThermoFisher | Cat#NP00061 |
| 1x Tris Buffered Saline (TBS) | Biorad | Cat#1610782 |
| Pierce™ ECL Plus Western Blotting Substrate | ThermoFisher | Cat#32132 |
| SuperSignal™ West Femto Maximum Sensitivity Substrate | ThermoFisher | Cat#34095 |
| NGS-WNT | Immunoprecise | Cat#N001 |
| EGF | Peprotech | Cat#AF-100-15 |
| A83-01 | Tociris | Cat#2939 |
| FGF2 | Peprotech | Cat#100-18B |
| IGF-1 | Peprotech | Cat#100-11 |
| Noggin Condition Media | Immunoprecise | Cat#N002 |
| R-Spondin 1 Conditioned Media | Made in Ganesh lab with R-Spondin1-Fc 293T line | |
| Alexa Fluor™ 488 Phalloidin | ThermoFisher | Cat#A12379 |
| Critical commercial assays | ||
| Visium Spatial gene Expression Starter Kit | 10X Genomics | Cat#1000200 |
| Mix-n-Stain 568/591 nm | Biotium | Cat#92336 |
| Click-iT™ EdU Cell Proliferation Kit for Imaging, Alexa Fluor™ 647 dye | ThermoFisher | Cat#C10340 |
| LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit, for 405 nm excitation | ThermoFisher | Cat#L34957 |
| Mouse Reelin ELISA Kit (Colorimetric) | Novus Biologic | Cat#NBP2-82424; RRID: |
| In Situ Cell Death Detection Kit, TMR red | Roche | Cat#12156792910 |
| Direct-zol RNA Microprep | Zymo Research | Cat#R2062 |
| Direct-zol RNA Miniprep | Zymo Research | Cat#R2050 |
| SuperScript™ VILO™ cDNA Synthesis Kit | ThermoFisher | Cat#11754050 |
| Power SYBR™ Green PCR Master Mix | ThermoFisher | Cat#4368577 |
| Pierce™ BCA Protein Assay Kit | ThermoFisher | Cat#23225 |
| Deposited data | ||
| Raw single and spatial transcriptomic data (mouse small and large intestine) | This paper | GEO: GSE190037 |
| Raw bulk RNA-sequencing data (mouse large intestine) | This paper | GEO: GSE199082 |
| Re-analyzed bulk RNA-sequencing data (mouse skin) | (Gur-Cohen et al., 2019) | GEO: GSE130976 |
| Re-analyzed single cell RNA-sequencing data (human) | (Elmentaite et al., 2021) | EMBL-EBI Array Express: E-MTAB-9532, E-MTAB-8901 |
| Experimental models: Cell lines | ||
| C57BL/6 MOUSE PRIMARY DERMAL LYMPHATIC ENDOTHELIAL CELLS | Cell Biologics | Cat#C57-6064L |
| B129 Mouse Primary Dermal Microvascular Endothelial Cells | Cell Biologics | Cat#B129-7064 |
| Human Dermal Lymphatic Endothelial Cells (HDLEC) - adult, cryopreserved | PromoCell | Cat#C-12217 |
| Experimental models: Organisms/strains | ||
| Mouse: C57BL/6J | The Jackson Laboratory | 000664 |
| Mouse: Lgr5-EGFP-IRES-CreERT2 (B6.129P2-Lgr5tm1(cre/ERT2)Cle/J) | The Jackson Laboratory | 008875 |
| Mouse: PDGFRa-H2B-EGFP (B6.129S4-Pdgfratm11(EGFP)Sor/J) | The Jackson Laboratory | 007669 |
| Mouse: ROSAmT/mG (Gt(ROSA)26Sortm4 (ACTB-tdTomato,-EGFP)Luo/J)) | The Jackson Laboratory | 007676 |
| Mouse: B6.Cg- Tg(Grem1-cre/ERT)3Tcw/J | The Jackson Laboratory | 027039 |
| Mouse: Vegfr3-CreERT2 iDTRflox/+ mice and Vegfr3-CreERT2 iDTRflox/+ tdTomatoflox/+ mice | (Gardenier et al., 2016) | N/A |
| Oligonucleotides | ||
| Quantitative real-time PCR primers (see table S1) | Eurofins Genomics | N/A |
| RNAscope® 2.5 LS Probe - Mm-Sox9-C2 - Mus musculus SRY-box containing gene 9 (Sox9), mRNA | ACD | 401058-C2 |
| RNAscope® 2.5 LS Probe - Mm-Lyz1-C3 - Mus musculus lysozyme 1 (Lyz1) mRNA | ACD | 415138-C3 |
| RNAscope® LS 2.5 Probe - Mm-Lgr5 - Mus musculus leucine rich repeat containing G protein coupled receptor 5 (Lgr5), mRNA | ACD | 312178-C1 |
| Software and algorithms | ||
| Prism | https://www.graphpad.com/scientific-software/prism/ | N/A |
| Imaris | https://imaris.oxinst.com/ | N/A |
| ImageJ | https://fiji.sc/ | N/A |
| FlowJo | https://www.flowjo.com | N/A |
| Biorender | https://biorender.com/ | N/A |
| Cellranger (version 6.0.1) | https://10xgenomics.com | N/A |
| Spaceranger (version 1.2.1) | https://10xgenomics.com | N/A |
| BayesPrism (R package) (version 1.3) | (Chu et al., 2022) | N/A |
| SpaceFold (R package) (version 1.0) | This paper: DOI 10.6084/m9.figshare.19715029 | N/A |
| phateR (R package) (version 1.0.7) | (Moon et al., 2019) | N/A |
| MAST (R package) (version 1.18.0) | (Finak et al., 2015) | N/A |
| biomaRt (R package) (version 2.48.3) | (Durinck et al., 2005, 2009) | N/A |
| miloR (R package) (version 1.0.0) | (Dann et al., 2021) | N/A |
| RCTD (R package) (version 1.2.0) | (Cable et al., 2021) | N/A |
| SPOTlight (R package) (version 0.99.8) | (Elosua-Bayes et al., 2021) | N/A |
| slalom (python package) (version 1.0.0.dev11) | (Buettner et al., 2017) | N/A |
| ForceAtlas2 (python package) (version 0.3.5) | (Jacomy et al., 2014) | N/A |
| scanpy (python package) (version 1.8.1) | (Wolf et al., 2018) | N/A |
| Phenograph (python package) (version 1.5.7) | (Levine et al., 2015) | N/A |
| scran (python package) (version 1.20.1) | (Lun et al., 2016) | N/A |
| mclust (python package) (version 5.4.7) | (Scrucca et al., 2016) | N/A |
| mixtools (python package) (version 1.2.0) | (Benaglia et al., 2010) | N/A |
| CellBender (python package) (version 1.0) | (Fleming et al., 2019) | N/A |
| DoubletDetection (python package) (version 3.0) | (Gayoso and Shor, 2020) | N/A |
| Scrublet (python package) (version 0.2.3) | (Wolock et al., 2019) | N/A |
| Stereoscope (python package) (version 0.3.1) | (Andersson et al., 2020) | N/A |
| Cell2location (python package) (version 0.6a0) | (Kleshchevnikov et al., 2022) | N/A |
| tangram-sc (python package) (version 1.0.1) | (Biancalani et al., 2021) | N/A |
| Other | ||
| BD FACSAria Cell Sorter | BD Bioscience | N/A |
| BD LSRII Analyzer | BD Bioscience | N/A |
| Synergy Neo2 Multi-Mode Reader | BioTek | |