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 |
| Rat monoclonal anti-CD24 PE [M1/69, BD] | Thermo Fisher Scientific | (BD Biosciences Cat# 553261, RRID:AB_394740) |
| Rat monoclonal anti-CD24 FITC [M1/69, BD] | Thermo Fisher Scientific | (BD Biosciences Cat# 561079, RRID:AB_2034001) |
| Rabbit monoclonal anti-SP-C [EPR19839] | Abcam | Cat# ab211326 |
| Goat polyclonal anti-SPC (M-20) | Santa Cruz Biotechnology | Cat# sc-7706; RRID:AB_2185507 |
| Goat polyclonal anti-CC10 (T-18) | Santa Cruz Biotechnology | Cat# sc-9772, RRID:AB_2238819 |
| Mouse monoclonal anti-CC10 (B-6) | Santa Cruz Biotechnology | Cat# sc-390313, |
| Mouse monoclonal anti-acetylated tubulin | Sigma-Aldrich | (Sigma-Aldrich Cat# T7451, RRID:AB_609894) |
| Mouse monoclonal anti-Histone H3 (di methyl K9) | Abcam | (Abcam Cat# ab1220, RRID:AB_449854) |
| Rabbit polyclonal anti-Di-Methyl Histone H3 (Lys9) | Cell Signaling Technologies | (Cell Signaling Technology Cat# 9753, RRID:AB_659848) |
| Rabbit polyclonal antiHistone H3 Trimethyl (Lys27) | Cell Signaling Technologies | (Cell Signaling Technology Cat# 9733, RRID:AB_2616029) |
| Mouse monoclonal anti 5-Methylcytosine [33D3] | Epigentek | Cat# 33m3 |
| Mouse monoclonal anti-acetyl-Histone H3 | EMD-Millipore | (Millipore Cat# 06-599, RRID:AB_2115283) |
| Chicken polyclonal anti-GFP | Abcam | (Abcam Cat# ab13970, RRID:AB_300798) |
| Chicken polyclonal anti-Keratin-5 | Biolegend | Biolegend Cat#Poly9059 |
| Hamster monoclonal anti-Podoplanin | Abcam | (Abcam Cat# ab11936, RRID:AB_298718) |
| Rat monoclonal anti-Ki-67 | Thermo Fisher Scientific | (Thermo Fisher Scientific Cat# 14-5698-82, RRID:AB_10854564) |
| Donkey anti-rabbit Alexa Fluor 488 | Thermo Fisher Scientific | (Thermo Fisher Scientific Cat# A-21206, RRID:AB_2535792) |
| Donkey anti-goat Alexa Fluor 594 | Thermo Fisher Scientific | (Thermo Fisher Scientific Cat# A-11058, RRID:AB_2534105) |
| Donkey anti-goat Alexa Fluor 647 | Thermo Fisher Scientific | (Thermo Fisher Scientific Cat# A-21447, RRID:AB_2535864) |
| Donkey anti-mouse Alexa Fluor 594 | Thermo Fisher Scientific | (Thermo Fisher Scientific Cat# A-21203, RRID:AB_141633) |
| Goat anti-mouse Alexa Fluor 647 | Thermo Fisher Scientific | (Thermo Fisher Scientific Cat# A-21235, RRID:AB_2535804) |
| Goat anti-rat Alexa Fluor 647 | Thermo Fisher Scientific | (Thermo Fisher Scientific Cat# A-21247, RRID:AB_141778) |
| Goat anti-chicken Alexa Fluor 594 | Thermo Fisher Scientific | (Thermo Fisher Scientific Cat# A-11042, RRID:AB_2534099) |
| Goat anti-hamster Alexa Fluor 647 | Thermo Fisher Scientific | (Thermo Fisher Scientific Cat# A-21451, RRID:AB_2535868) |
| Bacterial and virus strains | ||
| Ad5CMVCre | UI Viral Vector Core | VVC-U of Iowa 5 |
| Ad5CMVempty | UI Viral Vector Core | VVC-U of Iowa 272 |
| Chemicals, peptides, and recombinant proteins | ||
| UNC 0638 | Tocris | Cat# 4343 |
| UNC 0642 | Tocris | Cat# 5132/10 |
| Bleomycin Sulfate | Sigma-Aldrich | Cat# B2434 |
| Naphthalene | Sigma-Aldrich | Cat# 84679-1G |
| Corn Oil | Sigma-Aldrich | Cat# C8267-500ML |
| Dispase | Corning | Cat# 354235 |
| Collagenase/Dispase | Roche | Cat# 10269638001 |
| Dnase | Sigma-Aldrich | Cat# D4527 |
| Insulin Transferrin Selenium (ITS) | Corning | Cat# 25-800-CR |
| Growth Factor Reduced Matrigel | Corning | Cat# 356231 |
| Critical commercial assays | ||
| TDE I - transposase for ATAC-seq | Illumina | Cat# 15027865 |
| NEBNext High-Fidelity 2X PCR Master Mix | New England Biolabs | Cat# M0541S |
| NEBnext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) - 96 rxns | New England Biolabs | Cat# E6440S |
| Vectastain elite ABC mouse IgG | Vector Laboratories | Cat#PK-6102 |
| Deposited data | ||
| Single Cell RNA-seq data | Angelidis et al. 201932 | GEO: GSE124872 |
| ATAC-seq data | This study | GEO: GSE231366 |
| Experimental models: Organisms/strains | ||
| C57BL/6J | The Jackson Laboratory | Cat# 000664 |
| B6.Cg-Tg(CAG-DsRed∗MST)1Nagy/J (DsRed.T3) | The Jackson Laboratory | Cat# 6051 |
| B6.129X1-Gt(ROSA)26Sortm1(EYFP)Cos/J (YFP) | The Jackson Laboratory | Cat# 006148 |
| G9afl/fl | Anne Schaefer Laboratory, Mount Sinai University | N.A. |
| G9afl/fl YFP | This Study | N.A. |
| B6.129S-Sftpctm1(cre/ERT2)Blh/J (SPC-CreER) | The Jackson Laboratory | Cat# 028054 |
| SPC-CreER YFP | This Study | N.A. |
| SPC-CreER G9afl/fl YFP | This Study | N.A. |
| Software and algorithms | ||
| Image J | NIH | https://imagej.nih.gov/ij/ |
| GraphPad Prism | GraphPad Software | https://www.graphpad.com/scientific-software/prism/ |
| FlowJo |
Becton, Dickinson & Company |
https://www.flowjo.com/ |
| FASTQC | Andrews et al. 201057 | http://www.bioinformatics.babraham.ac.uk/projects/fastqc |
| Atropos | Didion et al. 201758 | https://github.com/jdidion/atropos |
| Bowtie2 | Langmead et al. 200959 | https://bowtie-bio.sourceforge.net/bowtie2/index.shtml#:~:text=Bowtie%202%20is%20an%20ultrafast,long%20(e.g.%20mammalian)%20genomes. |
| Deeptools | Ramirez et al. 201461 | https://deeptools.readthedocs.io/en/develop/ |
| Samtools | Li et al. 200962 | http://www.htslib.org/ |
| MACS2 | Zhang et al. 200863 | https://pypi.org/project/MACS2/ |
| ChIPQC | Carrol et al. 201464 | https://bioconductor.org/packages/release/bioc/html/ChIPQC.html |
| DiifBind | Stark et al. 201165 | https://bioconductor.org/packages/release/bioc/html/DiffBind.html |
| Bedtools | Qunilan et al. 201067 | https://bedtools.readthedocs.io/en/latest/ |
| ChIPseeker | Yu et al. 201568 | https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html |
| GREAT | McLean et al. 201069 | http://great.stanford.edu/public/html/ |
| MEME | Bailey et al. 200970 | https://meme-suite.org/meme/ |
| Seurat | Rahul Satija Laboratory | https://satijalab.org/seurat/ |
| Other | ||
| ProLongGold Antifade Mountant with DAPI | Thermo Fisher Scientific | Cat# P36935 |
| DAPI | Sigma-Aldrich | Cat# D9542 |
| Transwell Tissue Culture plate | Corning | Cat# 3470 |
| Qubit dsDNA HS Assay Kit | Thermo Fisher Scientific | Cat# Q32851 |
| DMEM | Gibco | Cat# 11995-065 |
| DMEM/F12 | Gibco | Cat# 11330-057 |
| HEPES | Thermo Fisher Scientific | Cat# 15630-080 |
| Penicillin-Streptomycin | Gibco | Cat# 15140-122 |
| Histogel | Thermo Fisher Scientific | Cat# HG4000012 |