KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rat monoclonal anti-CD45 APC [30-F11, BD] | Thermo Fisher Scientific | Cat# BDB559864; RRID:AB_398672 |
| Rat monoclonal anti-CD31 APC [MEC 13.3, BD] | Thermo Fisher Scientific | Cat# BDB551262; RRID:AB_398497 |
| Rat monoclonal anti-CD326 (Ep-CAM) PE/Cy7 [G8.8] | Biolegend | Cat# 118216; RRID:AB_1236471 |
| Rat monoclonal anti-Ly-6A/E (Sca1) APC/Cy7 [D7] | Thermo Fisher Scientific | Cat# 560654; RRID:AB_1727552 |
| Rabbit monoclonal anti-SP-C [EPR19839] | Abcam | Cat# ab211326 |
| Goat polyclonal anti-SPC (M-20) | Santa Cruz Biotechnology | Cat# sc-7706; RRID:AB_2185507 |
| Mouse monoclonal anti-RFP (RF5R) | Invitrogen | Cat# MA5-15257; RRID:AB_10999796 |
| Rabbit polyclonal anti-CC10 (FL-96) | Santa Cruz Biotechnology | Cat# sc-25555; RRID:AB_2269914 |
| Rat monoclonal anti-Sox2 (Btjce) | eBioscience | Cat# 14-9811-82; RRID:AB_11219471 |
| Rabbit monoclonal anti-p63-α (D2K8X) | Cell Signaling Technology | Cat# 13109S; RRID:AB_2637091 |
| Rat monoclonal anti-cytokeratin-8 | Developmental Studies Hybridoma Bank | Cat# TROMA-I; RRID:AB_531826 |
| Rabbit monoclonal anti-Keratin 17 (D73C7) | Cell Signaling Technology | Cat# 4543; RRID:AB_2133014 |
| Rat monoclonal anti-Brdu [BU1/75 (ICR1)] | Abcam | Cat# ab6326; RRID:AB_305426 |
| Rabbit monoclonal anti-Acetyl-α-Tubulin (Lys40) (D20G3) | Cell Signaling Technology | Cat# 5335; RRID:AB_10544694 |
| Mouse monoclonal anti-HopX antibody (E-1) | Santa Cruz Biotechnology | Cat# 398703; RRID:AB_2687966 |
| Donkey anti-rat Alexa Fluor 488 | Invitrogen | Cat# A-21208; RRID:AB_141709 |
| Donkey anti-rat Alexa Fluor 594 | Invitrogen | Cat# A-21209; RRID:AB_2535795 |
| Donkey anti-goat Alexa Fluor 488 | Invitrogen | Cat# A-11055; RRID:AB_2534102 |
| Donkey anti-rabbit Alexa Fluor 488 | Invitrogen | Cat# A-21206; RRID:AB_2535792 |
| Donkey anti-rabbit Alexa Fluor 594 | Invitrogen | Cat# A-21207; RRID:AB_141637 |
| Donkey anti-mouse Alexa Fluor 647 | Invitrogen | Cat# A-31571; RRID:AB_162542 |
| Chemicals, peptides, and recombinant proteins | ||
| Growth Factor Reduced Matrigel | Corning | Cat# 356231 |
| Bleomycin Sulfate | Sigma-Aldrich | Cat# B2434 |
| Dispase | Corning | Cat# 354235 |
| Collagenase/Dispase | Roche | Cat# 10269638001 |
| DNase | Sigma-Aldrich | Cat# D4527 |
| 0.25% Trypsin-EDTA | Invitrogen | Cat# 25200-056 |
| ITS | Corning | Cat# 25-800-CR |
| BrdU | Sigma-Aldrich | Cat# B9285 |
| Critical commercial assays | ||
| FITC BrdU Flow Kit | BD | Cat# 559619 |
| Chromium Single Cell 3′ Library & Gel Bead Kit v3, 16 reactions | 10x Genomics | Cat# 1000075 |
| Chromium Chip B Single Cell Kit, 48 reactions | 10x Genomics | Cat# PN-10000153 |
| Chromium i7 Sample Index Plate - 96 reactions | 10x Genomics | Cat# 220103 |
| Deposited data | ||
| Single cell RNA-seq raw data | This paper | GEO: GSE190565 |
| Single cell RNA-seq features/matrix/barcode files | This paper | GEO: GSE190565 |
| Jupyter notebooks for single cell RNA-Seq analysis | This paper | https://github.com/alm8517/Lung_organoid_transplantation |
| Experimental models: Organisms/strains | ||
| Hsd:Athymic Nude-Foxn1nu (Nude) | ENVIGO | Cat# 6903F |
| B6.129S7-Rag1tm1Mom/J (Rag1 KO) | The Jackson Laboratory | Cat# 02216 |
| B6.Cg-Tg(CAG-DsRed*MST)1Nagy/J (DsRed.T3) | The Jackson Laboratory | Cat# 6051 |
| Software and algorithms | ||
| Image J | Schneider et al. (2012) | https://imagej.nih.gov/ij/ |
| GraphPad Prism | GraphPad Software | https://www.graphpad.com/scientific-software/prism/ |
| FlowJo | Becton, Dickinson & Company | https://www.flowjo.com/ |
| Scanpy 1.4.6 | Wolf et al. (2018) Genome Biology | https://github.com/theislab/scanpy |
| Velocyto 0.17.17 | La Manno et al. (2018) Nature | https://github.com/velocyto-team/velocyto.py |
| scVelo 0.2.1 | Theis lab | https://github.com/theislab/scvelo |
| CellRanger 3.1.0 | 10X Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation |
| Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 | van Dijk et al. (2018) Cell | https://github.com/KrishnaswamyLab/MAGIC |
| Scanorama 1.6 | Hie et al. (2019) Nature Biotechnology | https://github.com/brianhie/scanorama |
| Other | ||
| ProLongGold Antifade Mountant with DAPI | Invitrogen | Cat# P36935 |
| DAPI | Sigma-Aldrich | Cat# D9542 |
| Transwells | Corning | Cat# 3470 |
| SPRIselect Reagent | Beckman Coulter | Cat# NC0406407 |
| Qubit dsDNA HS Assay Kit | Invitrogen | Cat# Q32851 |
| DMEM/F12 | Gibco | Cat# 11330-057 |
| DMEM | Gibco | Cat# 11995-065 |
| HEPES | Invitrogen | Cat# 15630-080 |
| Penicillin-Streptomycin | Gibco | Cat# 15140-122 |
| Histogel | Thermo Scientific | Cat# HG4000012 |