KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit monoclonal anti-Notch3 (D11B8) | Cell Signaling | Cat# 5276 RRID: AB_10560515 |
| Goat polyclonal anti-Klf4 | R&D | Cat# AF3640. RRID: AB_2130224 |
| Rabbit polyclonal anti-AP-2γ | Cell Signaling | Cat# 2320. RRID: AB_2202287 |
| Mouse monoclonal anti-Grhl3 (C12) | Santa Cruz | Cat# sc398838. RRID: N/A |
| Rabbit polyclonal anti-Kdm1a | Abcam | Cat# ab17721. RRID: AB_443964 |
| Rabbit polyclonal anti-Histone 3 (monomethyl K4) | Abcam | Cat# ab8895. RRID: AB_306847 |
| Rabbit polyclonal anti-Histone 3 (dimethyl K4) | Abcam | Cat# ab7766. RRID: ABB_2560996 |
| Mouse monoclonal anti-Keratin 14 | Abcam | Cat# ab7800. RRID: N/A |
| Rabbit polyclonal anti-Collagen VII | Millipore | Cat# 234192. RRID: AB_211739 |
| Mouse monoclonal anti-Involucrin (SY5) | Abcam | Cat# ab68. RRID: AB_305656 |
| Rabbit polyclonal anti-Filaggrin | Abcam | Cat# ab81468. RRRID: AB_1640512 |
| Rabbit polyclonal anti-IgG | Abcam | Cat# ab46540. RRID: AB_2614925 |
| Rabbit monoclonal anti-Slug (C19G7) | Cell Signaling | Cat# 9585. RRID: AB_2239535 |
| Rabbit monoclonal anti-CDK4 | Cell Signaling | Cat# 12790 |
| Rabbit monoclonal anti-p-ERK | Cell Signaling | Cat# 4370P |
| Bacterial and Virus Strains | ||
| Retrovirus: LZRS-ER-H-RAS G12V | Duperret et al., 2015; PMID 26359297 | N/A |
| Retrovirus: LZRS-Cdk4 R24C | Duperret et al., 2015; PMID 26359297 | N/A |
| Biological Samples | ||
| Primary epidermal progenitors (neonatal human epidermal keratinocytes, NHEKs) | Penn Skin Biology and Diseases Resources-based Center (SBDRC) | https://dermatology.upenn.edu/sbdrc/ |
| NHEKs transfected with CDK4 R24C and ER-H-RAS G12V expression | Penn Skin Biology and Diseases Resources-based Center (SBDRC) and Duperret et al., 2015; PMID 26359297 | N/A |
| Primary Normal Adult Human Dermis | Penn Skin Biology and Diseases Resources-based Center (SBDRC) | https://dermatology.upenn.edu/sbdrc/ |
| Chemicals, Peptides, and Recombinant Proteins | ||
| LSD1 inhibitor; GSK-LSD1 | Cayman Chemical | Cat# 16439 |
| LSD1 inhibitor; 2-PCPA | BPS Bioscience | Cat# 27305 |
| 4-hydroxytamoxifen | Sigma-Aldrich | Cat# H7904–5MG |
| Critical Commercial Assays | ||
| RNeasy Kit | QIAGEN | Cat# 74106 |
| NEBNext Poly(A) mRNA magnetic isolation module | New England Biolabs | Cat# E7490S |
| NEBNext Ultra Directional RNA Library Prep Kit for Illumina | New England Biolabs | Cat# E7420L |
| NEBNext Oligos for Illumina (Index Primer Set 1) | New England Biolabs | Cat# E7335L |
| NEBNext Oligos for Illumina (Index Primer Set 2) | New England Biolabs | Cat# E7500S |
| NEBNext Library Quantification Kit for Illumina | New England Biolabs | Cat# E7630L |
| NEBNext Ultra II DNA Library Prep Kit for Illumina | New England Biolabs | Cat# E7645L |
| High Sensitivity DNA Chips | Agilent Technologies | Cat# 5067–4626 |
| Deposited Data | ||
| All datatsets form this study | This study | GEO: GSE133766 |
| RNA-seq NHEK LSD1 inhibitors | This study | GEO: GSE133737 |
| RNA-seq NHEK Differentiation versus Proliferation | This study | GEO: GSE133738 |
| ChIP-seq NHEK LSD1 | This study | GEO: GSE133560 |
| Experimental Models: Cell Lines | ||
| J2 3T3 Fibroblasts | Kerafast | Cat# EF3003 |
| Phoenix cells-AMPHO | ATCC | Cat# CRL-3213 |
| Oligonucleotides | ||
| LSD1 targeted siRNA: SMARTpool: Accell KDM1A siRNA | Dharmacon | Cat# E-009223–00-0005 |
| Non-targeting control siRNA: Accell Non-Targeting Control siRNA | Dharmacon | Cat# D-001910–01-20 |
| Recombinant DNA | ||
| ER-H-RAS G12V | Duperret et al., 2015; PMID 26359297 | N/A |
| Cdk4 R24C | Duperret et al., 2015; PMID 26359297 | N/A |
| Software and Algorithms | ||
| STAR | Dobin et al., 2013; PMID 23104886 | https://doi.org/10.1093/bioinformatics/bts635 |
| DESeq2 | Love et al., 2014; PMID 25516281 | https://doi.org/10.1186/s13059–014-0550–8 |
| Bowtie2 V2–1.0 | PMID 22388286 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| HOMER v4.10.1 | Heinz et al., 2010; PMID 20513432 | https://doi.org/10.1016/j.molcel.2010.05.004 |
| http://homer.ucsd.edu/homer/ | ||
| BEDtools v2.27.1 | Quinlan and Hall 2010; PMID 20110278. | https://bedtools.readthedocs.io/en/latest/# |
| Quinlan, 2014; PMID 25199790 | https://doi.org/10.1093/bioinformatics/btq033 | |
| https://doi.org/10.1002/0471250953.bi1112s47 | ||
| macs2 v2.1.1.20160309 | Zhang et al., 2008; PMID 18798982 | https://github.com/taoliu/MACS |
| R version 3.5.0 | https://www.r-project.org/ | |
| R Studio version 1.1.383 | https://www.rstudio.com/ | |
| ImageJ | Schneider et al., 2012; PMID 22930834 | https://imagej.nih.gov/ij/ |
| NextSeq500 | https://www.illumina.com/systems/sequeseque-platforms/nextseq.html | |
| Illumina BaseSpace | https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub.html | |
| UCSC Genome Brower | Kent et al., 2002; PMID 12045153 | https://genome.ucsc.edu |
| PANTHER | Mi et al., 2019; PMID 30804569 | https://doi.org/10.1093/nar/gky1038 |
| http://www.pantherdb.org | ||
| Other | ||
| Keratinocyte-SFM (1X) | GIBCO | Cat# 10724–011 |
| Medium 154 | GIBCO | Cat# M-154–500 |
| Human Keratinocyte Growth Supplement (100X) | GIBCO | Cat# S-001–5 |
| Supplements For Keratinocytes –SFM | GIBCO | Cat# 37000–015 |
| Protein G Dynabeads | Thermo Fisher | Cat# 10004D |
| Benzonase Nuclease | Sigma | Cat# E1014–5KU |
| DMEM high glucose 4.5 g/L | Mediatech | Cat# MT10–013-CV |
| Ham’s F-12 | Lonza | Cat# 12–615F |
| Fetal Bovine Serum | Life Technologies | Cat# 16000–044 |
| Adenine hydrochloride hydrate | Sigma-Aldrich | Cat# A9795–5G |
| Hydrocortisone | Sigma-Aldrich | Cat# H4001–1G |
| Insulin from bovine pancreas | Sigma-Aldrich | Cat# I1882–100MG |
| Cholera Toxin from Vibrio cholerae | Sigma-Aldrich | Cat# C8052–0.5MG |
| EGF Human Recombinant | Invitrogen | Cat# PHG0311L |
| 3,3ʹ,5 Triido-L-thyronine | Sigma-Aldrich | Cat# T2877–100MG |
| Transferrin human | Sigma-Aldrich | T8158–100MG |
| Matrigel Matrix | Corning | Cat# 354234 |