| Antibodies |
| rabbit-anti-phospho-histone H3 (Ser10) |
Santa Cruz Biotechnology |
sc-8656-R |
| chicken-anti-mCherry |
Novus Biologicals |
NBP2-25158 |
| chicken-anti-GFP |
Abcam |
ab13970 |
| mouse-anti-MF-20 |
Developmental Studies Hybridoma Bank |
MF 20 |
| rabbit-anti-Sox9 |
Novus Biologicals |
NBP1-85551 |
| Alexa Fluor 488 anti-chicken |
ThermoFisher |
A-11039 |
| Alexa Fluor 568 anti-chicken |
ThermoFisher |
A-11041 |
| Alexa Fluor 568 anti-rabbit |
ThermoFisher |
A11011 |
| Alexa Fluor 647 anti-rabbit |
ThermoFisher |
A-31573 |
| Alexa Fluor 647 anti-mouse |
ThermoFisher |
21242 |
| Chemicals, Peptides, and Recombinant Proteins |
| Alexa Fluor 647 Phalloidin |
ThermoFisher |
A22287 |
| Critical Commercial Assays |
| RNAscope Multiplex Fluorescent Reagent Kit v2 Assay |
Advanced Cell Diagnostics |
Protocol 323100-USM and technical note MK 50-016 |
| Chromium Next GEM Single Cell Multiome ATAC + Gene Expression |
10X Genomics |
Protocol CG000338
|
| Deposited Data |
| Raw sequencing fastq files and Cell Ranger ARC v2.0.0-processed Multiome data in this paper |
GEO (Gene Expression Omnibus), this paper |
GSE210251 |
| Published scRNAseq of submandibular salivary gland |
GEO (Gene Expression Omnibus) (Hauser et al., 2020)28
|
GSE150327 |
| Published scRNA-Seq of mouse mandible |
FaceBase (Yuan et al., 2020)26
|
Record ID 1-DTK2 |
| Published ATAC-Seq of zebrafish NCC |
GEO (Gene Expression Omnibus) (Trinh et al., 2017)34
|
GSE89670 |
| Experimental Models: Organisms/Strains |
| Mouse: Nr5a2-flox: Nr5a2tm1Sakl
|
The Jackson Laboratory |
JAX 024054 |
| Mouse: Wnt1-Cre: Wnt1-Cre1 |
(Danielian et al., 1998)45
|
N/A |
| Mouse: Prrx1-Cre: Tg(Prrx1-Cre)1Cjt
|
The Jackson Laboratory |
JAX 005584 |
| Mouse: Scx-GFP: Tg(Scx-GFP)1Stzr
|
(Pryce et al., 2007)46
|
N/A |
| Zebrafish: nr5a2oz3: nr5a2oz3
|
(Nissim et al., 2016)23
|
oz3
|
| Zebrafish: sox10:dsRed:Tg(sox10:DsRedExpress)
|
Our lab |
el10
|
| Zebrafish: fli1a:GAL4:Tg(fli1:GAL4-VP16,myl7:EGFP)
|
Our lab |
el360
|
| Zebrafish: sox10:mGFP:Tg(sox10:EGFP-CAAX)
|
Our lab |
el375
|
| Zebrafish: col2a1a:GFP:TgBAC(col2a1a:EGFP) |
Our lab |
el483
|
| Zebrafish: col2a1a:mCherry:TgBAC(col2a1a:mCherry-NTR)
|
Our lab |
el599
|
| Zebrafish: col2a1a:h2az2a-mCherry-2A-EGFP-CAAX:Tg(col2a1a:h2az2a-mCherry-2A-EGFP-CAAX)
|
Our lab |
el690
|
| Zebrafish: scxa:mCherry:Tg(scxa:mCherry)
|
(Chen et al., 2020)43
|
fb301
|
| Zebrafish: actb2:LOXP-BFP-LOXP-DsRed:Tg(actb2:LOXP-BFP-LOXP-DsRed)
|
(Kobayashi et al., 2014) 44
|
sd27
|
| Zebrafish: nr5a2mGFP :Tg(nr5a2:GFP-CAAX)
|
This paper |
el874
|
| Zebrafish: nr5a2mGFP-DBD-del:Tg(nr5a2:GFP-CAAX-DBD-del)
|
This paper |
el875
|
| Zebrafish: UAS-nr5a2:Tg(UAS-nr5a2,cryaa:Cerulean)
|
This paper |
el877
|
| Zebrafish: foxp2-p1:GFP:Tg(foxp2_p1-Mmu.E1b:GFP, cryaa:Cerulean)
|
This paper |
el887,el888,el889
|
| Zebrafish: cdh6-p1:GFP:Tg(cdh6_p1-Mmu.E1b:GFP, cryaa:Cerulean)
|
This paper |
el895,el896,el897
|
| Zebrafish: fgf10a-p1:GFP:Tg(fgf10a_p1-Mmu.E1b:GFP, cryaa:Cerulean)
|
This paper |
el890,el891,el892
|
| Zebrafish: scxa-p2:GFP:Tg(scxa_p2-Mmu.E1b:GFP, cryaa:Cerulean)
|
This paper |
el900,el901
|
| Oligonucleotides |
| RNAscope probe: cdh6
|
Advanced Cell Diagnostics |
1225191-C4 |
| RNAscope probe: fgf10a
|
Advanced Cell Diagnostics |
1090101-C1, 1090101-C4 |
| RNAscope probe: foxp2
|
Advanced Cell Diagnostics |
1181381-C1 |
| RNAscope probe: nr5a2
|
Advanced Cell Diagnostics |
578901-C2 |
| RNAscope probe: ogna
|
Advanced Cell Diagnostics |
848241-C4 |
| RNAscope probe: sox9a
|
Advanced Cell Diagnostics |
543491-C3 |
| RNAscope probe: Nr5a2
|
Advanced Cell Diagnostics |
543571 |
| RNAscope probe: Sox9
|
Advanced Cell Diagnostics |
401051-C3 |
| guideRNA targeting sequences |
Table S6
|
N/A |
| In situ hybridization probes |
Table S6
|
N/A |
| Zebrafish transgenesis primers |
Table S6
|
N/A |
| Genotyping primers |
Table S6
|
N/A |
| Software and Algorithms |
| Cell Ranger ARC v2.0.0 |
10X Genomics |
https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc
|
| Seurat v4 |
(Hao et al., 2021)55
|
https://satijalab.org/seurat/
|
| Signac v1.6 |
(Stuart et al., 2021)56
|
https://satijalab.org/signac/
|
| chromVAR |
(Schep et al., 2017)57
|
https://greenleaflab.github.io/chromVAR/
|
| LinkPeaks |
(Ma et al., 2020)58
|
N/A |
| DAVID Bioinformatics Resources |
(Huang et al., 2009)59; (Sherman et al., 2022)60
|
https://david.ncifcrf.gov/
|
| Fiji |
(Schindelin et al., 2012)61
|
https://fiji.sc
|
