KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-ACTB | Abcam | Cat#ab8227 |
| anti-LC3B | Sigma-Aldrich | Cat#L7543 |
| anti-p62/SQSTM1 | Abcam | Cat#ab56416 |
| anti-HIF1A | BD | Cat#610959 |
| anti-HIF1B/ARNT | BD | Cat#611079 |
| anti-HIF2A | Novus Biologicals | Cat#NB100-122 |
| anti-BNIP3 | Abcam | Cat#ab109362 |
| anti-TUBB | Abcam | Cat#ab6046 |
| anti-Mouse IgG, HRP-conjugated | MP Biomedical | Cat#0855550 |
| anti-Rabbit IgG, HRP-conjugated | MP Biomedical | Cat#0855676 |
| anti-p62 | MBL | Cat#M162 |
| anti-LC3 | Novus Biological | Cat#NB100-2220 |
| anti-LC3 | Cell Signaling Technology | Cat#2775S |
| Bacterial and virus strains | ||
| Salmonella enterica serovar Typhimurium strain SL1344 | Lab stock | DSM 24522 |
| Chemicals, peptides, and recombinant proteins | ||
| Rapamycin | Thermo-Fisher | Cat#J62473 |
| Streptomycin sulfate | Sigma-Aldrich | Cat#S6501 |
| Phoshate buffered saline (PBS) | Thermo-Fisher | Cat#10010023 |
| LB-Miller broth | BD | Cat#244610 |
| Agar | BD | Cat#214010 |
| Glycerol | Sigma-Aldrich | Cat#G5516-500ML |
| IMDM | Corning | Cat#10-016-CV |
| GlutaMAX | Thermo-Fisher | Cat#35050061 |
| Penicillin/streptomycin | Thermo-Fisher | Cat#15140122 |
| Bovine calf serum | Cytiva | Cat#SH30072.03 |
| TRIzol reagent | Thermo-Fisher | Cat#15596026 |
| iScript Supermix reagent | Bio-Rad | Cat#1708841 |
| 2× Power SYBR Green | Thermo-Fisher | Cat#4367659 |
| SDS-PAGE sample buffer | Bio-Rad | Cat#1610747 |
| HALT Protease Inhibitor | Thermo-Fisher | Cat#78438 |
| Clarity Max ECL reagent | Bio-Rad | Cat#1705062 |
| ProLong Gold Anti-Fade reagent | Thermo-Fisher | Cat#P36930 |
| Critical commercial assays | ||
| Oxodish oxygen sensor plates | Presens | Cat#OD24 |
| EZ-10 DNAaway RNA Miniprep Kit | Bio Basic | Cat#BS88136 |
| Dual Luciferase Assay kit | Promega | Cat#E1960 |
| FuGENE HD | Promega | Cat#E2311 |
| Deposited data | ||
| HIF-1α and HIF-2α ChIP-chip profiling in intestinal epithelial cells | NCBI GEO | Accession#GSE43108 |
| Experimental models: Cell lines | ||
| HeLa | Lab stock | RRID:CVCL_0030 |
| C2BBe1 | Lab stock | RRID:CVCL_1096 |
| Colonoids | Healthy C57BL/6 mice | Generated in-house according to established protocols |
| Experimental models: Organisms/strains | ||
| Hif1b-flox/villin-cre | Lab colony | Previously generated (PMID# 24248342) |
| C57BL/6J wild-type | Lab colony | RRID:IMSR_JAX:000664 |
| ODD-luciferase | Lab colony | Previously described (PMID# 24412613) |
| Oligonucleotides | ||
| Primers | This publication | See Table S1 for sequences |
| anti-HIF1A shRNA | Functional Genomics Facility (Aurora, CO) | Accession#TRCN0000003811 |
| anti-HIF1B shRNA | Functional Genomics Facility (Aurora, CO) | Accession#TRCN0000003819 |
| anti-HIF2A shRNA | Functional Genomics Facility (Aurora, CO) | Accession#TRCN0000003806 |
| Recombinant DNA | ||
| pGL4.22-VEGF-HRE::dLUC | Chi Van Dang, via Addgene | RRID:Addgene_128096 |
| tf-LC3 | Tamotsu Yoshimori, via Addgene | RRID:Addgene_21074 |
| Software and algorithms | ||
| LinRegPCR | Untergasser et al. (PMID# 34433408) | n/a |
| ClustVis | Metsalu and Vilo (PMID# 25969447) | n/a |