Genetic reagent (M. musculus) | Shhtm1amc (Shh+/−) | Jackson Laboratory (Lewis et al., 2001) | Jackson Cat# 003318, MGI Cat# 3584154, RRID:MGI:3584154 | Swiss Webster background |
Genetic reagent (M. musculus) | Cg-Shhtm1(EGFP/cre)Cjt (ShhGFP-Cre) | Jackson Laboratory (Harfe et al., 2004) | Jackson Cat#: 005622; MGI Cat#: 92505; RRID: IMSR_JAX:005622 | Mixed background |
Genetic reagent (M. musculus) | Ptch1tm1Mps/J (PtchLacZ) | Jackson Laboratory (Goodrich et al., 1997) | Jackson Cat#: 003081; MGI Cat#: 42441; RRID: IMSR_JAX:003081 | BL6-background |
Genetic reagent (M. musculus) | Gli1tm2Alj/J (Gli1LacZ) | Laboratory of Dr. Aaron Zorn | Jackson Cat#: 008211; MGI Cat#: 2449767; RRID: IMSR_JAX: 008211 | |
Genetic reagent (M. musculus) | B6.129S6-Shhtm2(cre/ERT2)Cjt/J (ShhCreER/+) | Laboratory of Dr. Susan Mackem (Harfe et al., 2004) | Jackson Cat#: 005623 MGI: 92504 RRID: IMSR_JAX:005623 | Swiss Webster background |
Genetic reagent (M. musculus) | B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J (Rosa26Ai9/+) | Jackson Laboratory | Jackson Cat#: 007909 MGI: 155793 RRID: IMSR_JAX: 007909 | BL6-background |
Genetic reagent (M. musculus) | Swiss Webster Wildtype | Charles River | Charles River Cat# NCI 551 IMSR Cat# TAC:sw, RRID:IMSR_TAC:sw | |
Chemical compound, drug | Tamoxifen | Sigma-Aldrich | Cat#: T5648-1G Lot/batch#: WXBD2299V | |
Other | Trizol | Life Technologies | Cat#: 10296010 | Used for RNA extraction |
Commercial assay, kit | NEBNext Ultra II Directional RNA library prep kit | New England Biolabs | Cat#: E7760L | |
Commercial assay, kit | In Situ Cell death detection Kit | Roche | Cat# 12156792910 Lot#: 11520500 | OCT and paraffin |
Other | 4′,6-Diamidino-2-phenylindole (DAPI) | Invitrogen | Cat# D1306 Lot#: 2208529 | Nuclear stain for OCT and paraffin sections and whole mounts (1:5000) |
Other | Prolong Gold Antifade | Thermo Fisher Scientific | Cat#: P36930 | Used to mount OCT/paraffin section stains |
Chemical compound, drug | Histodenz | Sigma-Aldrich | Cat#: D2158-100G Lot #: WXBD3838V | Used to clear whole-mount embryos |
Chemical compound, drug | N-Methyl-acetimide | Sigma-Aldrich | Cat#: M26305-100G | Used to clear whole-mount embryos |
Other | Low-melt agarose | Sigma-Aldrich | Cat#: A2576-5G Lot#: SLCG3476 | Used at 1.5% agarose in water (wt/vol) |
Antibody | SOX9 (rabbit polyclonal) | Millipore | Cat#: AB5535; Lot#: 3389351 RRID:AB_2239761 | OCT and paraffin (1:200) |
Antibody | SOX2 (mouse monoclonal) | Santa-Cruz | Cat#: sc-365823; LOT#: E1619 RRID:AB_10842165 | OCT and paraffin (1:200) |
Antibody | NKX2.1 (TTF-1) (mouse monoclonal) | Santa-Cruz | Cat#: sc-53136 LOT#: B2219 RRID:AB_793529 | OCT (1:200) |
Antibody | FOXA2 (rabbit monoclonal) | Abcam | Cat#: ab108422; LOT#: GR3289185 RRID:AB_11157157 | OCT and paraffin (1:300) |
Antibody | FOXA2 (mouse monoclonal) | DSHB | Cat#: 4c7 RRID:AB_528255 | OCT (1:50) |
Antibody | N-Cadherin (rabbit monoclonal) | Cell Signaling Technologies | Cat#: 13116S RRID:AB_2687616 | OCT (1:200) |
Antibody | E-Cadherin (rabbit monoclonal) | Cell Signaling Technologies | Cat#: 3195S RRID:AB_2291471 | OCT and paraffin (1:200) |
Antibody | Vimentin (rabbit monoclonal) | Cell Signaling Technologies | Cat#: 5741T RRID:AB_10695459 | OCT (1:200) |
Antibody | P63 (mouse monoclonal) | Abcam | Cat#: ab735 RRID:AB_305870 | OCT and paraffin (1:200) |
Antibody | Cleaved-Caspase3 (D165) (rabbit monoclonal) | Cell Signaling Technologies | Cat#: 9664S RRID:AB_2070042 | OCT and paraffin (1:200) |
Antibody | GFP (chicken polyclonal) | Aves | Cat#: 1020; LOT#: 1229FP08 RRID:AB_10000240 | OCT (1:500) |
Antibody | RFP (Rabbit polyclonal) | Rockland | Cat#: 600-401-379; LOT#: 46317 RRID:AB_2209751 | OCT (1:100) |
Antibody | ECAD-488 (24E10) (rabbit monoclonal) | Cell Signaling Technologies | Cat#: 3199S RRID:AB_10691457 | OCT (1:200) |
Antibody | Phospho-Histone H3 (rabbit polyclonal) | Millipore | Cat#: 06-570; LOT#: 2972863 RRID:AB_310177 | OCT and paraffin (1:200) |
Antibody | Rabbit Isotype Control (DA1E) (rabbit monoclonal) | Cell Signaling Technologies | Cat#: 3900S RRID:AB_1550038 | OCT (4 μg/ml) |
Antibody | RAB-11 (rabbit monoclonal) | Cell Signaling Technologies | Cat#: 5589T RRID:AB_10693925 | OCT (1:100) |
Antibody | Beta-Catenin (rabbit polyclonal) | Thermo Fisher Scientific | Cat#: 71-2700 RRID:AB_2533982 | OCT (1:500) |
Antibody | Laminin (rabbit polyclonal) | Sigma-Aldrich | Cat#: L9393-100UL; LOT#: 099M4886V RRID:AB_477163 | Paraffin (1:100) |
Antibody | anti-Rabbit Alexa 488 (goatpolyclonal) | Thermo Fisher Scientific | Cat#: A11034 RRID:AB_2576217 | OCT and paraffin (1:250) |
Antibody | anti-Mouse Alexa 568 (goat polyclonal) | Thermo Fisher Scientific | Cat#: A11004 RRID:AB_2534072 | OCT and paraffin (1:250) |
Antibody | anti-Chicken Alexa 568 (goat polyclonal) | Thermo Fisher Scientific | Cat#: A11041 RRID:AB_2534098 | OCT (1:250) |
Antibody | anti-Rabbit Alexa 647 (goat polyclonal) | Life Technologies | Cat#: A27040 RRID:AB_2536101 | OCT (1:250) |
Commercial assay, kit | V3.0 HCR RNA-FISH Kit Probe Hybridization buffer | Molecular Instruments | LOT#: BPH02324 | Whole-mount embryos |
Commercial assay, kit | V3.0 HCR RNA-FISH Kit Probe Wash buffer | Molecular Instruments | LOT#: BPW02123 | Whole-mount embryos |
Commercial assay, kit | V3.0 HCR RNA-FISH Kit Amplification buffer | Molecular Instruments | LOT#: BAM01923 | Whole-mount embryos |
Commercial assay, kit | Cdh1 HCR probe (M. musculus) | Molecular Instruments | Probe Lot#: PRI679 MGI Accession: 12550 | Hairpin-B2-Alexa488 |
Commercial assay, kit | Cdh2 HCR probe (M. musculus) | Molecular Instruments | Probe Lot#: PRH832 MGI Accession: BC022107 | Hairpin-B1- Alexa594 |
Commercial assay, kit | Shh HCR probe (M. musculus) | Molecular Instruments | Probe Lot#: PRA909 MGI Accession: NM_009170 | Hairpin-B1-Alexa594 |
Commercial assay, kit | Pax1 HCR probe (M. musculus) | Molecular Instruments | Probe Lot#: PRH830 MGI Accession: NM_008780.2 | Hairpin-B1-Alexa594 |
Commercial assay, kit | Hoxb1 HCR probe (M. musculus) | Molecular Instruments | Probe Lot#: PRE343 | Hairpin-B4-Alexa647 |
Commercial assay, kit | Foxn1 HCR probe (M. musculus) | Molecular Instruments | Probe Lot#: PRN998 | Hairpin-B4-Alexa647 |
Software, algorithm | HISAT2 v2.1.0 | Pertea et al., 2016; Pertea et al., 2015 | RRID:SCR_015530 | Used for RNA-seq analysis |
Software, algorithm | StringTie v1.3.6 | Pertea et al., 2016; Pertea et al., 2015 | RRID:SCR_016323 | Used for RNA-seq analysis |
Software, algorithm | Imaris v9.9.1 software | Bitplane Inc | RRID:SCR_007370 | Used for 3D rendering of surfaces |