KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Armenian Hamster: phycoerythrin (PE)-conjugated ICAM1 | BD Pharmingen | Catalog No. 565615 |
| Rabbit: phycoerythrin (PE)-conjugated SCARB1 | Novus Biologicals | Catalog No. NB400-104PE |
| Rabbit: F3 | Bioss Antibodies | Catalog No. BS-4690R |
| Chicken: GFP/YFP | Abcam | Catalog No. ab13970 |
| Goat: SOX2 | Santa Cruz Biotechnology | Catalog No. SC17320 |
| Donkey anti-Goat: Alexa-594 conjugated secondary antibody | Thermo Fisher Scientific | Catalog No. A-11058 |
| Donkey anti-Chicken: Alexa-488 conjugated secondary antibody | Jackson ImmunoResearch | Catalog No. 703-545-155 |
| Donkey anti-Rabbit: Alexa-555 conjugated secondary antibody | Thermo Fisher Scientific | Catalog No. A-31572 |
| Donkey anti-Rabbit: Alexa-568 conjugated secondary antibody | Thermo Fisher Scientific | Catalog No. A-21207 |
| Donkey anti-Mouse IgG: Alexa-568 conjugated secondary antibody | Thermo Fisher Scientific | Catalog No. A-10037 |
| Donkey anti-Mouse IgG: Alexa-647 conjugated secondary antibody | Thermo Fisher Scientific | Catalog No. A-31571 |
| Donkey anti-Goat: Alexa-647 conjugated secondary antibody | Thermo Fisher Scientific | Catalog No. A-21447 |
| Goat anti-Chicken: Alexa-488 conjugated secondary antibody | Thermo Fisher Scientific | Catalog No. A-11039 |
| Goat anti-Mouse IgG: Alexa-633 conjugated secondary antibody | Thermo Fisher Scientific | Catalog No. A-21050 |
| Goat anti-Rabbit: Alexa-568 conjugated secondary antibody | Thermo Fisher Scientific | Catalog No. A-11011 |
| Goat anti-Armenian Hamster: Dylight 594 conjugated secondary antibody | Jackson ImmunoResearch | Catalog No. 127-515-099 |
| Mouse: P63 (4A4) | BioCare | Catalog No. CM163B |
| Goat: NEUROD1 | Santa Cruz Biotechnology | Catalog No. SC1084 |
| Mouse: NTUB/TuJ1 | Neuromics | Catalog No. MO-15013 |
| Rabbit: SOX9 | Milipore | Catalog No. AB5535 |
| Armenian Hamster: CD54/ICAM1 | BD Pharmingen | Catalog No. 550287 |
| Alkaline phosphatase-conjugated anti-digoxygenin | Sigma | Catalog No. 11093274910 |
| Alkaline phosphatase-conjugated anti-fluorescein | Sigma | Catalog No. 11426338910 |
| Bacterial and Virus Strains | ||
| None. | ||
| Biological Samples | ||
| None. | ||
| Chemicals, Peptides, and Recombinant Proteins | ||
| tamoxifen | Sigma | T5648 |
| Neurobasal medium | Thermo Fisher Scientific | 21103049 |
| papain | Worthington Biochemical Corporation | LS003119 |
| fetal bovine serum | Thermo Fisher Scientific | 26140-087 |
| propidium iodide | Sigma | 81845 |
| tissue freezing medium | Fisher | 15-183-13 |
| goat serum | Jackson ImmunoResearch | 005000121 |
| donkey serum | Jackson ImmunoResearch | 017000121 |
| Hoechst 33342 | Thermo Fisher Scientific | H3570 |
| DAPI in Vectashield | Vector Laboratories | H-1500 |
| 5-ethynyl-2′-deoxyuridine (EdU) | Thermo Fisher Scientific | A10044 |
| Dig RNA labeling mix | Roche (sold by Sigma) | 1277073 |
| RNA Labeling Mix, Fluorescein | Roche (sold by Sigma) | 11685619910 |
| BCIP/NBT color development substrate | Promega | s3771 |
| SuperScript RTIII reverse transcriptase | Invitrogen (now Thermo Fisher Scientific) | 18080093 |
| Trizol | Invitrogen (now Thermo Fisher Scientific) | 10296-010 |
| DNase1 | Roche | 03539121103 |
| Critical Commercial Assays | ||
| C1 IFC for mRNA-seq (5–10 μM) | Fluidigm | 1005759 |
| C1 IFC for mRNA-seq (10–17 μM) | Fluidigm | 1005760 |
| C1 Single-Cell Auto Prep Kit for mRNA Seq | Fluidigm | 100-6209 |
| C1 Single-Cell Auto Prep Reagent Kit for mRNA Seq | Fluidigm | 100-6201 |
| SMARTer Ultra Low RNA Kit for the Fluidigm C1 System | Clontech | 634833 |
| Advantage 2 PCR Kit | Clontech | 639207 |
| Agilent High Sensitivity DNA Kit Reagents | Agilent | 5067-4626 |
| Nextera XT DNA Sample Preparation Kit | Illumina | FC-131-1096 |
| Nextera XT DNA Sample Preparation Index Kits A–D | Illumina | FC-131-2001-4 |
| Agencourt AMPure XP beads | Beckman Coulter | A63880 |
| Qubit dsDNA High Sensitivity Assay Kit | Life Technologies Molecular Probes | Q32854 |
| Tyramide Signal Amplification kit cy3 | Perkin-Elmer | NEL744001KT |
| Tyramide Signal Amplification kit FITC | Perkin-Elmer | NEL741001KT |
| Click-iT EdU Imaging Kit, Alex Fluor 647 | Thermo Fisher Scientific | C10340 |
| Deposited Data | ||
| Raw data, normalized counts matrix | GEO | GEO accession # GSE95601 |
| Scripts for analysis | GitHub | https://github.com/rufletch/p63-HBC-diff |
| Experimental Models: Cell Lines | ||
| None. | ||
| Experimental Models: Organisms/Strains | ||
| Mus musculus: CD-1 | Charles River | Strain code 022 |
| Mus musculus: C57BL/6 | JAX mouse services | Stock no. 000664 |
| Mus musculus: B6.129-Krt5-CreER(T2) | Indra et al., 1999 | N/A |
| Mus musculus: B6.129-Ascl1-CreER(T2) | JAX mouse services; Kim et al., 2011 | Stock no. 012882 |
| Mus musculus: B6.129-Trp63lox/lox | Mills et al., 2002 | N/A |
| Mus musculus: B6.129-Sox2eGFP | JAX mouse services; Arnold et al., 2011 | Stock no. 017592 |
| Mus musculus: B6.129-Ctnnb1lxEx3/+ | Harada et al., 1999 | N/A |
| Mus musculus: B6.129-Ctnnb1lox/lox | JAX mouse services; | Stock no. 004152 |
| Brault et al., 2001 | ||
| Mus musculus: B6.129-Rosa26eYFP | JAX mouse services; Srinivas et al., 2001 | Stock no. 006148 |
| Mus musculus: B6.129-Rosa26Confetti | JAX mouse services; Snippert et al., 2010 | Stock no. 013731 |
| Oligonucleotides | ||
| See Table S6 for sequences. | ||
| Recombinant DNA | ||
| None. | ||
| Software and Algorithms | ||
| ImageJ (Version 1.48v) | Schneider et al., 2012 | https://imagej.nih.gov |
| Bowtie2 (Version 2.2.9) | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Cufflinks (Version 2.2.1) | Trapnell et al., 2010 | cole-trapnell- lab.github.io/cufflinks/ |
| Trimmomatic (Version 0.3.2) | Bolger et al., 2014 | http://www.usadellab.org/cms/index.php?page=trimmomatic |
| Tophat2 (Version 2.1.1) | Kim et al., 2013 | http://ccb.jhu.edu/software/tophat/ |
| RSEM (Version 1.2.31) | Li and Dewey, 2015 | https://deweylab.github.io/RSEM/ |
| Kallisto (0.43.0) | Bray et al., 2016 | https://pachterlab.github.io/kallisto/ |
| featureCounts (Version 1.5.0-p3) | Liao et al., 2014 | http://bioinf.wehi.edu.au/featureCounts/ |
| FastQC (Version 0.3.2) | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | |
| Picard Tools (Version 2.5.0) | https://broadinstitute.github.io/picard/ | |
| samtools (Version 1.3.1) | Li et al., 2009 | http://www.htslib.org/ |
| R (Version 3.3.0) | https://www.R-project.org/ | |
| SCONE (Version 0.0.7) | This paper; Risso et al. (in preparation) | https://github.com/YosefLab/scone |
| clusterExperiment (Version 0.99.3-9001) | This paper; Purdom et al. (in preparation) | http://bioconductor.org/packages/clusterExperiment |
| Slingshot (Version 0.0.0.9005) | This paper; Street et al. (in preparation) | https://github.com/kstreet13/slingshot |
| limma (Version 3.28.19) | Smyth, 2004 | https://bioconductor.org/packages/limma |
| PathVisio (Version 3.2.4) | Kutmon et al., 2015; van Iersel et al., 2008 | https://www.pathvisio.org/ |
| Other | ||
| None. | ||