KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Ki67 | Cell Signaling | Cat #: D3B5; RPID: AB_2687446 |
| Purified Rabbit Anti-Mouse K14 | Gift: Juile Segre, NIH | N/A |
| Purified Chicken Anti-Mouse K14 | Gift: Juile Segre, NIH | N/A |
| Purified Mouse Anti-Mouse Fos | Santa Cruz Biotechnology | Cat #: sc271243; RPID: AB_10610067 |
| Slug (Snai2) | Cell Signaling | Cat #: C19G7; RRID:AB_2239535 |
| F4/80 | eBioscience | Cat #: 14-4801-82, RRID:AB_467558 |
| aSMA | Abcam | Cat #: ab5694 |
| Col17a1 | Abcam | Cat #: ab184996 |
| P63 | Santa Cruz Biotechnology | Cat #: sc-8343 RRID:AB_653763 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Collagenase | Sigma | Cat #: C9091 |
| HEPES | Fisher | Cat #: BP310 |
| Sodium Pyruvate | Fisher | Cat #: BP356 |
| DNase | Sigma | Cat #: DN25 |
| SytoxBlue | Thermo Fisher | Cat #: S34857 |
| Nuclease-free Water | Thermo Fisher | Cat #: AM9937 |
| Low TE Buffer | Thermo Fisher | Cat #: 12090-015 |
| Ethanol | Millipore Sigma | Cat #: E7023-500ML |
| 10% Tween 20 | Bio-Rad | Cat #: 1662404 |
| Glycerin | Ricca Chemical Company | Cat #: 3290-32 |
| QIAGEN Buffer EB | QIAGEN | Cat #: 19086 |
| Coumarin 6 | Sigma | Cat #: 546283 |
| DAPI | Thermo Fisher | Cat #: D1306 |
| DPBS | Corning Cellgro | Cat #: 21-031-CM |
| Krt14-Probe | ACD | Cat #: 422521-C3 |
| Trp63-Probe | ACD | Cat #: 464591-C2 |
| Cdkn1a-Probe | ACD | Cat #: 408551-C1 |
| Id1-Probe | ACD | Cat #: 312221-C3 |
| Col17a1-Probe | ACD | Cat #: 552141-C1 |
| Critical Commercial Assays | ||
| Chromium Single Cell 3′ Library & Gel Bead Kit v2 | 10x Genomics | Cat #: PN-120237 |
| Chromium Single Cell A Chip Kits | 10x Genomics | Cat #: PN-120236 |
| Chromium i7 Multiplex Kit | 10x Genomics | Cat #: PN-120262 |
| SPRIselect Reagent Kit | Beckman Coulter | Cat #: B23318 |
| Multiplex Fluorescent v2 system | ACD | Cat #: 323100 |
| Deposited Data | ||
| Raw scRNA-seq data | This paper | GEO: GSE142471 |
| Experimental Models: Organisms/Strains | ||
| Mouse: K14-Cre | Andl et al., 2004 | N/A |
| Mouse: ROSAmTmG, Gt(ROSA)26 Sortm4(ACTB-tdTomato,-EGFP)Luo | The Jackson Laboratory | Cat #: JAX 007576 |
| Mouse: C57BL/6J | The Jackson Laboratory | Cat #: JAX 000664 |
| Software and Algorithms | ||
| Cell Ranger 2.1.0 | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest |
| Seruat v2 | Satija et al., 2015 | https://satijalab.org/seurat |
| Monocle 2 | Qiu et al., 2017b | http://cole-trapnell-lab.github.io/monocle-release/ |
| Monocle 3 | Cao et al., 2019 | https://cole-trapnell-lab.github.io/monocle3/ |
| scEpath | Jin et al., 2018 | https://github.com/sqjin/scEpath |
| nlvelo | This paper | https://github.com/sqjin/nlvelo |
| Combat | Johnson et al., 2007 | https://www.bioconductor.org/packages/release/bioc/html/sva.html |
| UMAP | McInnes et al., 2018 | https://github.com/lmcinnes/umap |
| AnimalTFDB 2.0 | Zhang et al., 2015 | http://bioinfo.life.hust.edu.cn/AnimalTFDB/#!/ |
| Velocyto | La Manno et al., 2018 | https://github.com/velocyto-team/velocyto.R |
| DoubletDetection | Gayoso and Shor, 2018 | https://github.com/JonathanShor/DoubletDetection |
| SimFCS 4.0 | omicX | https://omictools.com/simfcs-tool |
| scikit-learn | A free Python library | https://scikit-learn.org/stable/ |
| BASC | Hopfensitz et al., 2012 | https://cran.r-project.org/web/packages/Binarize/index.html |