Appendix 1—key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information | |
|---|---|---|---|---|---|
| Genetic reagent (M. musculus) | C57BL/6J | Jackson lab | Stock #: 000664 | ||
| Genetic reagent (M. musculus) | Mettl3flox | PMID:31412241
J. Brüning (Max Planck Institute for Metabolism Research and Policlinic for Endocrinology, Diabetes and Preventive Medicine) |
|||
| Genetic reagent (M. musculus) | Krt14-Cre | PMID:10411913
E. Fuchs (Rockefeller University) |
MGI:1926500 | ||
| Genetic reagent (M. musculus) | Rosa26-YFPflox | Jackson lab | Stock #: 006148 | ||
| Genetic reagent (M. musculus) | Gli-LacZ | PMID:12361967
A. Joyner (MSKCC) |
MGI:2449767 | ||
| Genetic reagent (M. musculus) | Nude (Nu/Nu) | Charles River Laboratories | Strain code: 088 | ||
| Antibody | Rat anti-BrdU | Abcam | Cat. #: ab6326 RRID:AB_305426 |
IMF (1:200) | |
| Antibody | Rat anti-CD104 | BD Pharmingen | Cat. #: 553745 RRID: AB_395027 |
IMF (1:500) | |
| Antibody | Armenian hamster anti-CD29 | BioLegend | Cat. #: 102201 RRID:AB_312878 |
IMF (1:500) | |
| Antibody | Rat anti-CD49f | BioLegend | Cat. #: 313602 RRID:AB_345296 |
IMF (1:1000) | |
| Antibody | Rabbit anti-Cleaved Caspase-3 | R&D Systems | Cat. #: AF835 RRID:AB_2243952 |
IMF (1:200) | |
| Antibody | Rabbit anti-ECAD | Cell Signaling | Cat. #: 3195 RRID:AB_2291471 |
IMF (1:500) | |
| Antibody | Rabbit anti-FLG | E. Fuchs (Rockefeller University) | IMF (1:2000) | ||
| Antibody | Rabbit anti-HES1 | E. Fuchs (Rockefeller University) | IMF (1:200) | ||
| Antibody | Rabbit anti-iNV | BioLegend | Cat. #: 924401 RRID:AB_2565452 |
IMF (1:2000) | |
| Antibody | Guinea pig anti-K5 | E. Fuchs (Rockefeller University) | IMF (1:500) | ||
| Antibody | Rabbit anti-K10 | Covance | Cat. #: PRB-159P-100 RRID:AB_291580 |
IMF (1:1000) Flow (1:500) |
|
| Antibody | Guinea pig anti-LEF1 | E. Fuchs (Rockefeller University) | IMF (1:5000) | ||
| Antibody | Rabbit anti-LHX2 | E. Fuchs (Rockefeller University) | IMF (1:5000) | ||
| Antibody | Rabbit anti-LOR | E. Fuchs (Rockefeller University) | IMF (1:4000) | ||
| Antibody | Rabbit anti-METTL3 | Abcam | Cat. #: ab195352 RRID:AB_2721254 |
IMF (1:100-1:500) | |
| Antibody | Rabbit anti-MYC | Abcam | Cat. #: ab32072 RRID:AB_731658 |
IMF (1:100) | |
| Antibody | Goat anti-PCAD | R&D Systems | Cat. #: AF761 RRID:AB_355581 |
IMF (1:300-1:600) | |
| Antibody | Rabbit anti-SOX9 | Millipore | Cat. #: AB5535 RRID:AB_2239761 |
IMF (1:1000) | |
| Antibody | Rabbit anti-Survivin | Cell Signalling | Cat. #: 2808 RRID:AB_2063948 |
IMF (1:500) | |
| Antibody | Chicken anti-GFP/YFP | Abcam | Cat. #: ab13970 RRID:AB_300798 |
IMF (1:1000-1:1200) | |
| Antibody | anti-CD29 PECy7 | Thermo Fisher Scientific | Cat. #: 25-0291-82 RRID: AB_1234962 |
FACS (1:1000) | |
| Antibody | anti-CD31 APC | Thermo Fisher Scientific | Cat. #: 17-0311-82 RRID:AB_657735 |
FACS (1:1000) | |
| Antibody | anti CD45-APC | Thermo Fisher Scientific | Cat. #: 17-0451-83 RRID:AB_469393 |
FACS (1:1000) | |
| Antibody | anti-CD49f PE | Thermo Fisher Scientific | Cat. #: 12-0495-81 RRID:AB_891478 |
FACS (1:1000) | |
| Antibody | anti-CD49f PECy7 | Thermo Fisher Scientific | Cat. #: 25-0495-82 RRID:AB_10804881 |
FACS (1:1000) | |
| Antibody | anti CD117-APC | Thermo Fisher Scientific | Cat. #: 17-1172-81 RRID:AB_469432 |
FACS (1:1000) | |
| Antibody | anti CD140a-APC | Thermo Fisher Scientific | Cat. #: 17-1401-81 RRID:AB_529482 |
FACS (1:500) | |
| Antibody | Mouse anti-rabbit IgG PE-Cy7 | Santa Cruz | Cat. #: sc-516721 |
Flow (1:300) | |
| Chemical compound, drug | Alexa Fluor 647 Phalloidin | Thermo Fisher Scientific | Cat. #: A22287 RRID:AB_2620155 |
IMF (1:50) | |
| Commercial assay or kit | In situ cell death detection kit, TMR red | Sigma-Aldrich | Cat. #: 12156792910 | ||
| Commercial assay or kit | Click-iT EdU cell proliferation kit for imaging, Alexa Fluor 647 dye | Thermo Fisher Scientific | Cat. #: C10340 | ||
| Commercial assay or kit | LIVE/DEADfixable Aqua dead cell stain kit, for 405 nm excitation | Thermo Fisher Scientific | Cat. #: L34957 | ||
| Commercial assay or kit | Fixation/ permeabilization solution kit | BD Biosciences | Cat. #: 554714 | ||
| Commercial assay or kit | Dynabeads mRNA purification kit | Thermo Fisher Scientific | Cat. #: 61006 | ||
| Commercial assay or kit | Direct-zol RNA miniprep kit | Zymo Research | Cat. #: R2051 | ||
| Commercial assay or kit | RQ1 RNase-free DNase | Promega | Cat. #: M6101 | ||
| Commercial assay or kit | High-capacity cDNA reverse transcription kit | Thermo Fisher Scientific | Cat. #: 4368814 | ||
| Commercial assay or kit | Power SYBR Green PCR Master Mix | Thermo Fisher Scientific | Cat. #: 4367660 | ||
| Commercial assay or kit | Chromium single cell 3' reagent kit | 10x Genomics | Cat. #: PN-120267 | ||
| Chemical compound, drug | TRI Reagent LS |
Sigma-Aldrich | Cat. #: T3934 | ||
| Software, algorithm | Zen | Zeiss | https://www.zeiss.com/microscopy/int/products/microscope-software/zen.html | ||
| Software, algorithm | Fiji ImageJ | ImageJ | https://imagej.net/Fiji | ||
| Software, algorithm | Andor IQ3 | Oxford Instruments | https://andor.oxinst.com/products/iq-live-cell-imaging-software/ | ||
| Software, algorithm | GraphPad Prism 8.2 | GraphPad | https://www.graphpad.com/ | ||
| Software, algorithm | BD FACSDiva | BD Biosciences | https://www.bdbiosciences.com/en-us/instruments/research-instruments/research-software/flow-cytometry-acquisition/facsdiva-software | ||
| Software, algorithm | FlowJo | FlowJo, LLC | https://www.flowjo.com/solutions/flowjo | Version 10 | |
| Software, algorithm | R | CRAN | https://cran.r-project.org | R Version 3.6.3 Bioconductor Version 3.10 |
|
| Software, algorithm | Flexbar | PMID:24832523 | https://github.com/seqan/flexbar | Version 2.5 | |
| Software, algorithm | pyCRAC | S. Granneman (SynthSys) | http://sandergranneman.bio.ed.ac.uk/pycrac-software | Version 1.1.3 |
|
| Software, algorithm | Novoalign | Novocraft | http://www.novocraft.com/products/novoalign/ | Version 3.04.06 | |
| Software, algorithm | CIMS | C. Zhang (Columbia University) | https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation | ||
| Software, algorithm | Bedtools | PMID:20110278
A. Quinlan (University of Utah) |
https://github.com/arq5x/bedtools2.git | Version 2.25.0 | |
| Software, algorithm | Samtools | PMID:19505943
H. Li (Harvard University) |
http://samtools.sourceforge.net | Version 1.2 | |
| Software, algorithm | Cell Ranger | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome | Version 2.1.1 | |
| Software, algorithm | Seurat | PMID:29608179
R. Satija (New York University) |
https://satijalab.org/seurat/
|
Version 2.3.4 | |
| Software, algorithm | Monocle | PMID:28114287
C. Trapnell (University of Washington) |
http://cole-trapnell-lab.github.io/monocle-release/ | Version 2.10.1 | |
| Software, algorithm | MAST | PMID:26653891
A. McDavid (University of Rochester Medical Center) |
https://www.bioconductor.org/packages/release/bioc/html/MAST.html | Version 1.8.2 | |