KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-MUC5AC | Santa Cruz Biotechnology | Cat# sc-20118; RRID: AB_2146854 |
| Mouse monoclonal anti-Acetylated Tubulin | Sigma-Aldrich | Cat# T7451; RRID: AB_609894 |
| Rabbit polyclonal anti-Ki67 | Abcam | Cat# ab15580; RRID: AB_443209 |
| Mouse monoclonal anti-KRT14 | Thermo Fisher Scientific | Cat# MA5-11599; RRID: AB_10982092 |
| Rabbit monoclonal anti-YAP | Cell Signaling Technology | Cat# 14074; RRID: AB_2650491 |
| Alexa Fluor 594 Phalloidin | Thermo Fisher Scientific | Cat# A12381; RRID: AB_2315633 |
| Rabbit monoclonal anti-P63 | Cell Signaling Technology | Cat# 13109; RRID: AB_2637091 |
| ZO-1 Monoclonal Antibody (ZO1-1A12), Alexa Fluor 488 | Thermo Fisher Scientific | Cat# 339188; RRID: AB_2532187 |
| Occludin Monoclonal Antibody (OC-3F10), FITC | Thermo Fisher Scientific | Cat# 33-1511; RRID: AB_2533102 |
| Bacterial and Virus Strains | ||
| NucLight Red Lentivirus (EF-1 Alpha Promoter, Puromycin selection) | Essen Biosciences | Cat# 4476 |
| Biological Samples | ||
| Human foreskin tissue, fresh | Zenbio | Cat# T-FS |
| Human nasal brushing samples from CF patients | UNC CF Clinics | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Tocriscreen Stem Cell Toolbox | Tocris | Cat# 5060 |
| A83-01 | Sigma-Aldrich | Cat# SML0788 |
| Y-27632 dihydrochloride | Enzo Life Sciences | Cat# ALX-270-333 |
| Isoprenaline hydrochloride | Sigma-Aldrich | Cat# I5627-5G |
| (−)-Blebbistatin | Selleck Chemicals | Cat# S7099 |
| IPA-3 | Tocris | Cat# 3622 |
| GSK-429286 | Sigma-Aldrich | Cat# SML0231 |
| Critical Commercial Assays | ||
| Telomere length measurements by quantitative PCR service | Risques Lab at University of Washington | http://depts.washington.edu/risques/ |
| G-Band Karyotyping service | Cell Line Genetics | N/A |
| Whole genome sequencing service | Novogene | N/A |
| Ussing assays service | ChanTest, a subsidiary of Charles River Laboratories | N/A |
| Histology service (Paraffin section, H&E and alcian blue staining) | VitroVivo Biotech LLC | N/A |
| TGF-β ELISA service | University of Maryland Cytokine Core Lab | N/A |
| RT2 Profiler PCR Array Human Cellular Senescence | QIAGEN | Cat# PAHS-050ZA-6 |
| In vivo tumorigenicity service | Noble Life Sciences | N/A |
| Deposited Data | ||
| Raw and analyzed RNA-seq, MeDIP-seq and MRE-seq data | This paper | GSE103759 containing the Subseries GSE103756 (RNA-seq), GSE103757 (MeDIP-seq) and GSE103758 (MRE-seq) |
| Analyzed whole genome sequencing data | This paper | Figure 3; Table S4 |
| Experimental Models: Cell Lines | ||
| Human bronchial epithelial cells, P1, from healthy and CF donors | UNC CF Center Tissue Procurement and Cell Culture Core |
N/A |
| NHBE-Bronchial Epi Cells for B-ALI | Lonza | Cat# CC-2540S |
| CF-DHBE - Diseased Bronchial Epi. Cells (CF) | Lonza | Cat# 196979 |
| Human Epidermal Keratinocytes, adult (HEKa) | Thermo Fisher Scientific | Cat# C0055C |
| Human Epidermal Keratinocytes, neonatal (HEKn) | Thermo Fisher Scientific | Cat# C0015C |
| HMEC-Human Mammary Epithelial Cells | Lonza | Cat# CC-2551 |
| LNCap Clone FGC Cell Line human | Sigma-Aldrich | Cat# D-073-1ML |
| Human normal prostate epithelial cells | Georgetown University | N/A |
| Experimental Models: Organisms/Strains | ||
| Nude mice (Noble Life Sciences) | Jackson Lab | N/A |
| NSG mice (Noble Life Sciences) | Jackson Lab | N/A |
| Oligonucleotides | ||
| qRT-PCR primers for TERT (forward primer, 5′-TGACACCTCACCTCACCCAC-3′, reverse primer, 5′-CACTGTCTTCCGCAAGTTCAC-3′ and Taqman probe (5′-ACCCTGGTCCGAGGTGTCCCTGAG-3′) | This paper | N/A |
| Software and Algorithms | ||
| STAR, v.2.5.3a | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| featureCounts (Subread v.1.5.3) | Liao et al., 2014 | http://bioinf.wehi.edu.au/featureCounts/ |
| DESeq2 bioconductor package v.1.14.1 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Metascape | Tripathi et al., 2015 | http://metascape.org |
| BWA-MEM v.0.7.10 | Li, 2013 | http://bio-bwa.sourceforge.net/ |
| methylQA | Li etal., 2015 | http://methylqa.sourceforge.net/ |
| methylCRF | Stevens et al., 2013 | http://methylcrf.wustl.edu/ |
| methylMnM | Zhang et al., 2013 | http://bioconductor.org/packages/release/bioc/html/methylMnM.html |
| Predict cumulative population doublings using DNA methylation of 6 CpG sites | Koch and Wagner, 2013 | Figure 6 and Table S7 |
| Other | ||
| IncuCyte ZOOM System | Essen Biosciences | N/A |
| Data visualization in WashU Human Epigenome Browser | This paper | http://epigenomegateway.wustl.edu/browser/?genome=hg19&datahub=http://wangftp.wustl.edu/~hlee/EpiX/EpiX_hg19.json |