KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER | |||
|---|---|---|---|---|---|
| Antibodies | |||||
| GATA6 | Cell Signaling | 5851; RRID:AB_10705521 | |||
| GATA4 | Santa Cruz | SC-1237; RRID:AB_2108747 | |||
| FOXA2 | RnD | AF2400; RRID: AB_2294104 | |||
| SOX17 | RnD | AF1924; RRID:AB_355060 | |||
| OCT4 | Santa Cruz | SC-9081; RRID:AB_2167703 | |||
| HNF4A | Santa Cruz | SC-6556; RRID:AB_2117025 | |||
| EOMES | Cell Signaling | 66325; RRID: Unknown | |||
| CHD4 | Cell Signaling | 12011; RRID:AB_2734702 | |||
| SMARCA4 | Cell Signaling | 49360’ RRID:AB_2728743 | |||
| KDM1A | Cell Signaling | 2184; RRID:AB_2070132 | |||
| WDR5 | Cell Signaling | 13105; RRID:AB_2620133 | |||
| FLAG | Sigma-Aldrich | F1804; RRID:AB_262044 | |||
| Normal Mouse IgG | Sigma-Aldrich | 12-371; RRID:AB_145840 | |||
| H3K4me1 | Diagenode | C15410194; RRID:AB_2637078 | |||
| H3K9me2 | Abcam | ab1220; RRID:AB_449854 | |||
| H3K9me3 | Abcam | ab8898; RRID:AB_306848 | |||
| β-Actin | Sigma-Aldrich | A1978; RRID:AB_476692 | |||
| Bacterial and virus strains | |||||
| pzbFGF BL21 Star E. coli | Ludwig et al., 2006 | N/A | |||
| Chemicals, peptides, and recombinant proteins | |||||
| mTesR | Ludwig et al., 2006 | N/A | |||
| E-cadherin | Nagaoka et al., 2010 | N/A | |||
| RPMI 1640 | ThermoFisher Scientific | 22400089 | |||
| Geltrex | ThermoFisher Scientific | A1413302 | |||
| B-27 Supplement (50X), serum free | ThermoFisher Scientific | 17504044 | |||
| B-27 Supplement (50x), minus insulin | ThermoFisher Scientific | A1895601 | |||
| Activin A Recombinant Human Protein | ThermoFisher Scientific | PHC9563 | |||
| FGF-Basic (AA 10-155) Recombinant Human Protein |
ThermoFisher Scientific | PHG0023 | |||
| Purified recombinant zebrafish FGF-Basic | Ludwig et al., 2006 | N/A | |||
| BMP4 Recombinant Human Protein | ThermoFisher Scientific | PHC9533 | |||
| Formaldehyde 16%(w/v) | ThermoFisher Scientific | 28906 | |||
| Puromycin | Sigma-Aldrich | P9620 | |||
| Doxycycline hyclate | Sigma-Aldrich | D9891 | |||
| ROCK inhibitor Y27632 | StemRD | 146986-50-7 | |||
| DAPI | Sigma-Aldrich | D1388 | |||
| Critical commercial assays | |||||
| RNeasy mini Kit | QIAGEN | 74106 | |||
| TURBO DNA-free™ Kit | ThermoFisher/Ambion | AM1907 | |||
| M-MLV Reverse Transcriptase | ThermoFisher/Invitrogen | 28025-013 | |||
| TaqMan Gene Expression | ThermoFisher/Applied Biosystems | 4369016 | |||
| Pierce BCA protein assay kit | ThermoFisher Scientific | 23227 | |||
| Pierce Magnetic CHIP kit | ThermoFisher Scientific | 26157 | |||
| Transcription Factor Staining Buffer Set | ThermoFisher Scientific/eBioscience | 00-5523-00 | |||
| QuickExtract™ DNA extraction solution | Epicenter | QE09050 | |||
| Herculase II Fusion DNA Polymerase | Agilent Technologies | 600679 | |||
| Taq Polymerase | Sigma-Aldrich/Roche | 11146173001 | |||
| Deposited data | |||||
| ATAC-seq data | This paper | GEO: GSE156021 | |||
| RNA-seq data | This paper | GEO: GSE156021 | |||
| ChIP-seq: H3K4me1 | This paper | GEO: GSE156021 | |||
| ChIP-seq: H3K9me2 | This paper | GEO: GSE156021 | |||
| ChIP-seq H3K9me3 | This paper | GEO: GSE156021 | |||
| ChIP-seq GATA6 | This paper | GEO: GSE156021 | |||
| ChIP-seq FOXA2 | This paper | GEO: GSE156021 | |||
| ChIP-seq: EOMES | This paper | GEO: GSE156021 | |||
| Experimental models: Cell lines | |||||
| IPSC-K3 | Si-Tayeb et al., 2010b | N/A | |||
| IPSC-K3 GATA6Ex2Δ31/Δ38 | This paper | N/A | |||
| IPSC-K3 GATA6Ex4Δ1/Δ2 | This paper | N/A | |||
| IPSC-K3 GATA6Ex4Δ1/Δ2;indGATA6 | This paper | N/A | |||
| IPSC-K3 GATA6Ex4Δ1/Δ2;indFOXA2 | This paper | N/A | |||
| Oligonucleotides | |||||
| See Table S7 for oligonucleotides used | Integrated DNA Technologies | N/A | |||
| Recombinant DNA | |||||
| PX459 pSPCas9(BB)-2A-Puro vector | Ran et al., 2013 | Addgene Plasmid #62988 | |||
| pTET-Tight-GATA6-3xFLAG | Fisher et al., 2017 | N/A | |||
| pTET-Tight-FOXA2-3xFLAG | This paper | N/A | |||
| pGL4.20-TTR-3kb | This paper / Promega | E6751 | |||
| Software and algorithms | |||||
| TIDE | (Brinkman et al., 2014); https://tide.nki.nl/ | Version 2.0.1 | |||
| PANTHER classification system | (Mi et al., 2013); http://www.pantherdb.org/ | Version 15 | |||
| Graphpad with PRISM | https://www.graphpad.com/ | Version 8.4.2 | |||
| FlowJo | https://www.flowjo.com/ | Version 10.5.0 | |||
| EaSEQ | (Lerdrup et al., 2016); https://easeq.net/ | Version 1.111 | |||
| FastQC | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | Version 0.11.7 | |||
| Partek Flow | https://www.partek.com/partek-flow/ | Version 9.0.20.0526 | |||
| STAR | Partek Flow | Version 2.6.1d | |||
| BOWTIE2 | Partek Flow | Version 2.2.5 | |||
| MACS2 | Partek Flow | Version 2.1.1 | |||
| HOMER | (Heinz et al., 2010); http://homer.ucsd.edu/homer/ | Version 4.10 | |||
| Other | |||||
| Raw data (GATA6-birA ChIP-seq) | Fisher et al., 2017 | GEO: GSE77360 | |||
| Raw data (Endoderm TF ChIP-seq) | Tsankov et al., 2015 | GEO: GSE61475 | |||
| Raw data (KDM1A ChIP-seq) | Vinckier et al., 2020 | GEO: GSE104840 | |||
| Raw data (H3K4me2 and H3K27ac ChIP-seq) | Loh et al., 2014 | GEO: GSE52658 | |||
| Raw data (PDX1 ChIP-seq, pancreatic progenitor) | Lee et al., 2019 | GEO: GSE114102 | |||