KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-mouse CD3ε antibody | BioLegend | Clone: 145–2C11 |
| anti-mouse CD5 antibody | BioLegend | Clone: 53–7.3 |
| anti–mouse CD8 antibody | BioLegend | Clone: 53–5.8 |
| anti–mouse CD11b antibody | BioLegend | Clone: M1/70 |
| anti-mouse CD11c | BioLegend | Clone: N418 |
| anti–mouse CD19 antibody | BioLegend | Clone: 1D3 |
| anti-mouse CD25 antibody | BioLegend | Clone: PC61.5 |
| anti-mouse CD45.1 | BioLegend | Clone: A20 |
| anti-mouse CD45.2 | BioLegend | Clone: 104 |
| anti-mouse CD117 antibody | BioLegend | Clone: ACK2 |
| anti-mouse Ly6G antibody | BioLegend | Clone: 1A8 |
| anti-mouse F4/80 antibody | BioLegend | Clone: BM8 |
| anti-mouse FLT3 antibody | BioLegend | Clone: A2F10 |
| anti-mouse α4β7 antibody | BioLegend | Clone: DATK32 |
| anti-mouse NKp46 antibody | BioLegend | Clone: 29A1.4 |
| anti-mouse CCR6 antibody | BioLegend | Clone: 29–2L17 |
| anti-mouse KLRG1 antibody | BioLegend | Clone: 2FI |
| anti-mouse NK1.1 | BioLegend | Clone: PK136 |
| anti-mouse PD1 antibody | Bioxcell | Clone: J43 |
| anti–mouse CD127 antibody | BioLegend | Clone: A7R34 |
| anti–mouse RORγt antibody | BD Biosciences | Clone: Q31–378 |
| anti-mouse T-bet antibody | BioLegend | Clone: 4B10 |
| anti-mouse ZBTB16 antibody | BD Biosciences | Clone: R17–809 |
| anti-mouse TCF7 antibody | BioLegend | Clone: 812145 |
| anti-mouse GATA3 antibody | BioLegend | Clone: 16E10A23 |
| anti-mouse Id2 antibody | ThermoFisher | Clone: 17-9475-82 |
| anti-mouse Eomes antibody | ThermoFisher | Clone: TBR2 |
| anti-mouse BrdU antibody | BioLegend | Clone: Bu20a |
| anti–mouse CD4 antibody | BioLegend | Clone: GK1.5 |
| anti-mouse B220 | BioLegend | Clone: 2FI |
| anti-mouse FcεR1 blocking antibody | BD Biosciences | Clone: 93 |
| anti-CD131 | BD Biosciences | Clone: REA193 |
| anti-CD45.2 | BD Biosciences | Clone: V450 |
| anti-CD140 | BD Biosciences | Clone: APA5 |
| anti-CD326 antibody | BD Biosciences | Clone: G8.8 |
| anti- CD31 | BD Biosciences | Clone: MEC13.3 |
| anti-IGF1 | Santa Cruz | Clone: SC 461 |
| anti-IL33R | R&D Biosystems | Clone: AF1004 |
| anti-IgG | BioLegend | Clone: RMG1–1 |
| anti-mouse Sca1 | BioLegend | Clone: D7 |
| chicken anti-mouse GFP | ThermoFisher | Catalog: A10262 |
| rabbit anti-mouse NKX2.1 | Seven Hills Bioreagents | Clone: 1231 |
| mouse anti-mouse PDGFRα | ThermoFisher | Clone: APA5 |
| hamster anti-mouse IGF1 | Millipore | Clone: Sm1.2 |
| anti-human CD3 | BioLegend | Clone: UCHT1 |
| anti-human CD5 | BioLegend | Clone: UCHT2 |
| ant--human CD11c | BioLegend | Clone: S-HCL-3 |
| anti-human CD11b | BioLegend | Clone: M1/70 |
| anti-human CD19 | BioLegend | Clone: HIB19 |
| anti-human FcεRI | BioLegend | Clone: AER-37 |
| anti-human CD34 | BioLegend | Clone: 581 |
| ant-human CD14 | BioLegend | Clone: HCD14 |
| anti-human CD45 | BioLegend | Clone: HI30 |
| anti-human CD127 | BioLegend | Clone: A019D5 |
| isotype-matched control antibodies | BioLegend | Clone: MOPC-173 |
| anti-human GATA-3 | eBiosciences | Clone: TWAJ |
| anti-human RORγT | eBiosciences | Clone: AFKJS-9 |
| anti-human IL-22 antibody | eBiosciences | Clone: 22URTI |
| Bacterial and Virus Strains | ||
| S. pneumoniae serotype 19A | ATCC | Catalog: 700674 |
| Biological Samples | ||
| Preterm human infants diagnosed with bronchopulmonary dysplasia or term healthy infants. | CD45+ cells in Bronchial lavage fluid | NA |
| Chemicals, Peptides, and Recombinant Proteins | ||
| True Nuclear Transcription Factor Buffer | BioLegend | Catalog: 424401 |
| Zombie NIR fixable viability marker | BioLegend | Catalog: 423105 |
| Matrigel (growth factor reduced, phenol-red free) | Corning | Catalog: 356238 |
| Protein kinase (ROCK) inhibitor, Y-27632 | ThermoFisher | BDB562822 |
| murine IL-7 | R&D | Catalog: 407-ML-005 |
| stem cell factor | BioLegend | Catalog: 579702 |
| 1X Matrisperse Cell recovery solution | BD Biosciences | Catalog: 354253 |
| phorbol 12-myristate 13-acteate (PMA) | Sigma Aldrich | Catalog: P8139 |
| calcium ionophore A23187 | Sigma Aldrich | Catalog: C7522 |
| DMEM:F12 containing heavy and non-heavy 13C6 L-Lysine-2HCl | ThermoFisher | Catalog: 88439 |
| Critical Commercial Assays | ||
| Illumina TruSeq Stranded Total RNA kit | Illumina | RS-122–2201 |
| Deposited Data | ||
| Single-cell and time-course RNA-seq experiments from newborn lungs | NCBI SRA | GEO accession # GSE122332 |
| RNA-seq of sorted ZBTB16+ ILC precursors from newborn lungs and bone marrow | NCBI SRA | GEO accession # PRJNA599444 |
| Raw Data | Mendeley Data | http://dx.doi.org/10.17632/zkj6v7s8cp.1 |
| Experimental Models: Cell Lines | ||
| OP9-DL1 | Dr. J. C. Zúñiga-Pflücker | N/A |
| 3D Alveolar Aggregates | This manuscript | N/A |
| Experimental Models: Organisms/Strains | ||
| Zbtb16CreGFP | Jackson Laboratory | Stock # 024529 |
| RorcCreGFP | Jackson Laboratory | Stock # 022971 |
| Rosa26iDTR | Jackson Laboratory | Stock #007900 |
| Gli1CreER | Jackson Laboratory | Stock # 007913 |
| Igf1fl/fl | Jackson Laboratory | Stock # 016831 |
| Igf1rfl/fl | Jackson Laboratory | Stock # 012251 |
| Rag2−/−;Il2rg−/− | Jackson Laboratory | Stock # 014593 |
| B6 Cd45.1, Pep/BoyJ | Jackson Laboratory | Stock# 002014 |
| Il22fl/fl | mutant mouse resource and research center (MMRRC | Stock # 032402 |
| Software and Algorithms | ||
| FlowJo | Treestar | https://www.flowjo.com/ |
| ImageJ | ImageJ | https://imagej.nih.gov/ij/ |
| Imaris software | Bitplane | http://www.bitplane.com/ProductDetail.aspx?ProductID=57&SeriesId=55&Page=camera |
| Nikon Elements software | Nikon | https://www.microscope.healthcare.nikon.com/products/software/nis-elements |
| MaxQuant | https://www.maxquant.org/ | version 1.5.1.2 |
| Ensembl | https://useast.ensembl.org/info/website/archives/index.html | version GRCm38_71 (released April, 2013) |
| Perseus | https://omictools.com/perseus-tool | version1.5.8.5 |
| ToppGene Suite | https://toppgene.cchmc.org/https://toppgene.cchmc.org/ | https://toppgene.cchmc.org/ |
| NHLBI LungMAP | https://www.lungmap.net/about/lungmap-team/nhlbi/ | https://www.lungmap.net/about/lungmap-team/nhlbi/ |
| Illumina HiSeq 2500 | https://www.illumina.com/systems/sequencing-platforms/hiseq-2500.html | https://www.illumina.com/systems/sequencing-platforms/hiseq-2500.html |
| HISAT | http://www.ccb.jhu.edu/software/hisat/index.shtml | http://www.ccb.jhu.edu/software/hisat/index.shtml |
| Seurat | https://www.rdocumentation.org/packages/Seurat/versions/2.2.0 | version 2.2 |
| HISAT2 | https://ccb.jhu.edu/software/hisat2/index.shtml | https://ccb.jhu.edu/software/hisat2/index.shtml |
| Seqmonk | https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ | version 1.45.1 |
| Seqmonk | https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ | version 1.41.0 |
| Prism 6 | Graphpad | https://www.graphpad.com/scientific-software/prism/ |
| Other | ||
| LSRII | BD Biosciences | https://www.bd.com/resource.aspx?IDX=17868 |
| FACSAria II | BD Biosciences | https://www.bdbiosciences.com/documents/BD_FACSAria_II_cell_sorter_brochure.pdf |
| Nikon Eclipse confocal microscope | Nikon | https://www.microscope.healthcare.nikon.com/products/inverted-microscopes/eclipse-ti2-series |
| LTQ-OrbiTrap XL linear ion trap mass spectrometer | ThermoFisher | IQLAAEGAAVFACZMAIK |
| Sony SH800S | Sony Biotechnology | https://www.sonybiotechnology.com/us/instruments/sh800s-cell-sorter/ |