KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse anti-p53 (D0-1) | Millipore | Cat# OP43 |
| Rabbit anti-acetyl-p53 (K382) | Cell Signaling Technology | Cat#2525 |
| Rabbit anti-histone H2AX | Cell Signaling Technology | Cat#2595 |
| Rabbit anti-phospho-histone H2AX (Ser139) | Cell Signaling Technology | Cat#9718 |
| Rabbit anti-p53 antibody | Bethyl Laboratories Inc, | Cat#A300-247A |
| Mouse anti-p53 (pab240) | Abcam | Cat# AB26 |
| Mouse anti-p53 (pab240) | Novus Biologicals | Cat# NB200-103 |
| Rabbit anti-p73 | Bethyl laboratories | Cat# A300-126A |
| Rabbit anti-amyloid OC fibrils | Millipore | Cat#AB2286 |
| Mouse anti-β-actin | Sigma-Aldrich | Cat# A5441 |
| Goat anti-mouse IgG HRP | Promega | Cat# PAW4021 |
| D-11 scFv antibody | A gift from Dr. Raymond Mernaugh, Vanderbilt University, USA | N/A |
| Rabbit anti- E:tag antibody | Abcam | Cat# AB3415 |
| Bacterial and virus strains | ||
| H.pylori 7.13 | A gift from Dr. Richard Peek, Vanderbilt University Medical Center, USA | N/A |
| Biological samples | ||
| Human Tissue | Department of Pathology, University of Miami, USA | N/A |
| Mouse samples | University of Miami, USA | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| PI/RNase staining buffer | BD Biosciences | Cat# 550825 |
| Coomassie Brilliant Blue R-250 | Biorad | Cat# 1610400 |
| NAC (N-acetylcysteine) | Sigma-Aldrich | Cat# A0737 |
| TEMPOL (4-hydroxy-2,2,6,6-tetramethylpiperydine-1-oxyl) | Enzo Lifesciences | Cat# ALX-430-081-G001 |
| NS-398 | Cayman Chemical | Cat#70590 |
| 2-HOBA | Cayman Chemical | Cat#25357 |
| Critical commercial assays | ||
| p53 human immunocapture kit | Abcam | Cat# AB154470 |
| RNeasy Mini Kit | QIAGEN Inc | Cat#74134 |
| High-Capacity cDNA Reverse Transcription Kit | Applied Biosystems | Cat# 4368814 |
| RT2 Profiler PCR Array, Human p53 signaling pathway | QIAGEN Inc | Cat# 330231 |
| Magna ChIP A/G kit | Millipore | Cat# 17-10085 |
| Subcellular Protein Fractionation Kit | ThermoFisher Scientific | Cat#78840 |
| Proteostat Protein Aggregation Assay Kit | Enzo Lifesciences | Cat#ENZ-51023-KP050 |
| Dual Luciferase Reporter Assay Kit | Promega | E1910 |
| Deposited data | ||
| ChIP-Seq data | This manuscript | NCBI SRA (Sequence Read Archive); PRJNA912777 (https://dataview.ncbi.nlm.nih.gov/object/PRJNA912777?reviewer=6cnca4108s5od672ijo7001e36) |
| Experimental models: Cell lines | ||
| BAR-T (human Barrett’s epithelial cells) | A kind gift from Dr. Souza, Baylor University Medical Center, USA | N/A |
| CP-A (human Barrett’s epithelial cells) | ATCC (American Type Culture Collection) | Cat#CRL-4027 |
| EPC-2 (human normal epithelial cells) | A gift from Dr. Claudia Andl, University of Central Florida, USA | N/A |
| GES-1 (human normal gastric epithelial cells) | A kind gift from Dr. El-rifai, University of Miami USA | N/A |
| SNU-1 (human gastric epithelial cancer cells) | ATCC (American Type Culture Collection) | Cat# CRL-5971 |
| Experimental models: Organisms/strains | ||
| 129/sv mice | University of Miami | N/A |
| Oligonucleotides | ||
| HPRT Forward: 5′-TTGGAAAGGG TGTTTATTCCTCA-3′ Reverse: 5′- TCCAGCAGGTCAGCAAAGAA-3′ |
Integrated DNA Technologies (IDT) | N/A |
| p21 Forward: 5′-CTGGAGACTC TCAGGGTCGAAA-3′ Reverse: 5′-GA TTAGGGCTTCCTCTTGGAGAA-3′ |
Millipore Sigma | N/A |
| PUMA Forward: 5′-ACGACCTCAA CGCACAGTACG-3′ Reverse: 5′-TCC CATGATGAGATTGTACAGGAC-3′ |
Integrated DNA Technologies (IDT) | N/A |
| 5′-Biotinylated p21; 5-biotin-AG CCTCCCTCCATCCCTAT-3 and 5′-CCCTTCCTCACCTGAAAACA-3′ |
Vilgelm et al., 2010; Integrated DNA Technologies (IDT) | N/A |
| 5′-Biotinylated PUMA; 5′-biotin-CCC AGTCAGTGTGTGTGTCC-3′ and 5′-CCCCCGCGTGACGCTAC-3′ |
Vilgelm et al., 2010; Integrated DNA Technologies (IDT) | N/A |
| Non-specific probe,n/s, 5′-biotin-TA GCTGGGAAGCTGGGACTA-3′ and 5′-GGTTTCCTTGCCCTAAAAGG-3′ |
Vilgelm et al., 2010; Integrated DNA Technologies (IDT) | N/A |
| ChIP qPCR; p21 (5′-ACCTTTCA CCATTCCCCTAC-3′, 5′-GCCC AAGGACAAAATAGCCA-3′ |
Vilgelm et al., 2010; Millipore Sigma | N/A |
| ChIP qPCR; PUMA (5′-TGTCCA TGGTGTGGATTTGCG-3′, 5′-AGAC ACCGGGACAGTCGGACA-3′ |
Vilgelm et al., 2010; Millipore Sigma | N/A |
| Human p53 siRNA | Santa Cruz Biotechnology | Cat#sc-29435 |
| Software and algorithms | ||
| GeneGlobe Data Analysis Center provided by Qiagen Inc. | QIAGEN Inc. | https://geneglobe.qiagen.com/us/analyze |
| Open Comet software | Open Comet | https://cometbio.org/ |
| FCS express 7 | De Novo software | https://denovosoftware.com/ |
| GraphPad Prism 8.0.0 | GraphPad Software | https://www.graphpad.com/ |