Key Resources Table.
| Reagent or resource | Source | Identifier |
|---|---|---|
| Antibodies | ||
| Sox2-V450 | BD Biosciences | Cat#561610; clone O30-678 |
| Pax6-PerCPCy5.5 | BD Biosciences | Cat#562388; clone 018-1330 |
| Nkx6.1-AlexaFluor647 | BD Biosciences | Cat#563338; clone R11-560 |
| Goat anti-Olig2 | R&D | Cat#AF2418 |
| Nkx2.2-PE | BD Biosciences | Cat#564730; clone 74.5A5 |
| Tubb3-Biotin | BD Biosciences | Cat#560394; TUJ1 |
| Foxa2-AlexaFluor488 | SC Biotechnology | Cat#sc-374376 AF488; clone H-4 |
| Goat anti-Sox2 | R&D | Cat#AF2018 |
| Rat anti-Sox2 | Invitrogen | Cat#14-9811-80, clone Btjce |
| Mouse anti-Nkx2.2 | BD Biosciences | Cat#564731, clone 74.5A5 |
| Rabbit anti-Olig2 | Merck Millipore | Cat#AB9610 |
| Rabbit anti-Arx | Kind gift from J.Chelly | N/A |
| Goat anti-Foxa2 | R&D | Cat#AF2400 |
| Rabbit anti-Pax6 | Merck Millipore | Cat#AB2237 |
| Donkey anti-rat 405 | Biotium | Cat#20419 |
| Donkey anti-mouse AF488 | Invitrogen | Cat#A21202 |
| Donkey anti-goat AF488 | Invitrogen | Cat#A11055 |
| Donkey anti-rabbit AF488 | Invitrogen | Cat#A21206 |
| Strep-APC-Cy7 | BioLegend | Cat#405208 |
| Donkey anti-mouse AF568 | Invitrogen | Cat#A10037 |
| Donkey anti-goat AF568 | Invitrogen | Cat#A11057 |
| Donkey anti-mouse AF647 | Invitrogen | Cat#A31571 |
| Donkey anti-goat AF647 | Invitrogen | Cat#A21447 |
| Bacterial and virus strains | ||
| BL21-Gold(DE3) | Agilent | Cat#230132 |
| Chemicals, peptides, and recombinant proteins | ||
| Recombinant Mouse LIF Protein | Merck | Cat#ESG1107 |
| Dulbecco's Modified Eagle Medium (DMEM) - Knock OUT |
Gibco | Cat#10829-018 |
| ES Foetal Bovine Serum (FBS) | Pan Biotech | Cat#P30-2602 |
| Penicillin/Streptomycin | Gibco | Cat#15140122 |
| L-Glutamine | Gibco | Cat#25030024 |
| Non-essential amino acids | Gibco | Cat#11140-035 |
| 2-mercaptoethanol | Gibco | Cat#21985-023 |
| 0.05% trypsin-EDTA | Gibco | Cat#25300054 |
| Gelatin | Gibco | Cat#G1393-100ML |
| Advanced DMEM-F12 | Gibco | Cat#21331-020 |
| Neurobasal medium | Gibco | Cat#A35829-01 |
| N2 | Gibco | Cat#17502001 |
| B27 | Gibco | Cat#17504001 |
| Bovine Serum Albumin solution | Merck | Cat#A7979-50ML |
| Matrigel | Corning | Cat#356231 |
| bFGF | R&D | Cat#100-18B |
| LGK | Cayman Chemical Company | Cat#1.800.364.9897 |
| CHIR99021 | Axon Medchem | Cat#1386 |
| SB-431542 | Tocris | Cat#S0400 |
| DMH1 | Adooq Bioscience | Cat#A12820 |
| Retinoic Acid (RA) | Sigma | Cat#R2625 |
| Smoothened Agonist (SAG) | Merck | Cat#566660-5mg |
| DBZ | Biotechne | Cat#4489 |
| Doxycycline | Sigma-Aldrich | Cat#D9891 |
| Tamoxifen | Sigma-Aldrich | Cat#T5648-5G |
| Lipofectamine 2000 | Invitrogen | Cat#11668030 |
| Hygromycin-B | Thermo Fisher | Cat#10687010 |
| Puromycin | Thermo Fisher | Cat#A1113802 |
| LIVE/DEADTM Fixable Dead Cell Stain Near-IR fluorescent reactive dye |
ThermoScientific | Cat#L34976 |
| Phosphate Buffer Saline (PBS) | Gibco | Cat#14190-094 |
| Accutase | Gibco | Cat#00-4555-56 |
| Paraformaldehyde (PFA) | ThermoScientific | Cat#28908 |
| Triton-X100 | VWR Chemicals | Cat#28817.295 |
| Superscript III reverse transcriptase | Invitrogen | Cat#18080-051 |
| SYBR Green PCR assay | ThermoFisher Scientific | Cat#A25742 |
| ProLong Gold antifade reagent | Invitrogen | Cat#P36930 |
| Igepal CA-630 | Sigma | Cat#I8896-100ML |
| Tween-20 | Sigma | Cat#P2287-500ML |
| Digitonin | Invitrogen | Cat#BN2006 |
| Proteinase K | Ambion | Cat#AM2546 |
| 2X PCR Master Mix NEB | NEB | Cat#M0541S |
| AMPureXP beads | Beckman Coulter | Cat#A63882 |
| Ni-Sepharose column | Cytiva | Cat#17526801 |
| RNasin Plus | Promega | Cat#N2615 |
| Critical commercial assays | ||
| Zymo DNA concentrator kit | Zymo | Cat#D4013 |
| RecoverAll RNA/DNA Isolation Kit | Thermo Fisher Scientific | Cat#AM1975 |
| SMART-Seq HT kit | Takara | Cat#634437 |
| Nextera XT DNA Library Preparation Kit | Illumina | Cat#FC-131-1096 |
| TDE tagmentation enzyme | Illumina | Cat#15027865 |
| 2X TD tagmentation buffer | Illumina | Cat#15027866 |
| RNeasy Qiagen kit with DNAse digest | QIAGEN | Cat#74106 |
| Mouse Embryonic Stem Cell Nucleofector™ Kit |
Lonza | Cat#VPH-1001 |
| Deposited data | ||
| CaTS-ATAC, live Omni-ATAC, RNA-seq and bulk ATAC-seq |
This study | GSE204921 |
| Experimental models: Cell lines | ||
| Mus musculus (Male): HM1 | Doetschman et al.78 | N/A |
| Mus musculus (Male): HM1-Foxa2-/- | This study | N/A |
|
Mus musculus (Male): HM1-TetON-Foxa2- mCherry |
This study | N/A |
|
Mus musculus (Male): HM1-TetON- mCherry |
This study | N/A |
| Experimental models: Organisms/strains | ||
| Mouse: Foxa2nEGFP-CreERT2/+ | Imuta et al.46 | MGI:5490029 |
| Mouse: R26tdTomatoAi14/tdTomatoAi14 (Gt(ROSA)26Sortm14(CAG-tdTomato) Hze |
Madisen et al.79 | MGI:3809524 |
| Oligonucleotides | ||
| qPCR primers used in this study, see Table S1 |
N/A | |
| Primers for cloning of Foxa2 guides into pX458, see Table S1 |
This study | N/A |
| Oligonucleotides for Tn5 assembly, see Table S1 |
Picelli et al.80 | N/A |
| Oligonucleotides for CaTS-ATAC and ATAC-seq library, see Table S1 |
This study | N/A |
| Recombinant DNA | ||
| pX458 vector | Ran et al.81 | Addgene plasmid 48138 |
| PB-tetOn-destination-PGK-hygro | Stuart et al.82 | N/A |
| PB-CAG-rtTA3-PGK-puro | Stuart et al.82 | N/A |
| Software and algorithms | ||
| nf-core atacseq pipeline | https://nf-co.re/atacseq | https://doi.org/10.5281/zenodo.2634132 |
| DESeq2 | Love et al.83 | https://doi.org/10.18129/B9.bioc.DESeq2 |
| nf-core chipseq pipeline | https://nf-co.re/chipseq | https://doi.org/10.5281/zenodo.3240506 |
| TOBIAS footprinting tools | Bentsen et al.33 | https://doi.org/10.1038/s41467-020-18035-1 |
| nf-core rnaseq pipeline | https://nf-co.re/rnaseq | https://doi.org/10.5281/zenodo.1400710 |
| R | R Core Team | https://www.R-project.org/ |
| Fiji | Schindelin et al.84 | https://imagej.net/software/fiji/ |
| Other | ||
| Superfrost Plus slides | Thermo Scientific | Cat#10149870 |
| 22-mm-by-50-mm no. 1.5 thickness coverslips |
VWR | Cat#631-0138 |
| 6-well plates | Corning | Cat#353046 |
| LoBind 1.5 ml Eppendorf tubes | Eppendorf | Cat#Z666548 |
| DNA High Sensitivity DNA Kit | Agilent | Part No 5067-4626 |