KEY RESOURCES TABLE
| Reagent or resource | Source | Identifier |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal IgG1 anti-Pax7 | Developmental Studies Hybridoma Bank (DSHB) | Cat# PAX7, RRID:AB_528428 |
| Mouse monoclonal IgG1 anti-Cadherin-6B | Developmental Studies Hybridoma Bank (DSHB) | Cad# CCD6B-1, RRID:AB_531766 |
| Rabbit monoclonal anti-Slug (Snai2, Clone C19G7) | Cell Signaling Technologies | Cat# 9585, RRID:AB_2239535 |
| Rabbit polyclonal anti-Sox9 | Sigma-Aldrich | Cat# AB5535, RRID:AB_2239761 |
| Rabbit monoclonal anti-Laminin (LAMA1) | Sigma-Aldrich | Cat# L9393, RRID:AB_477163 |
| Mouse monoclonal IgG1 anti-FLAG (Clone M2) | Sigma-Aldrich | Cat# F1804, RRID:AB_262044 |
| Rabbit anti-Phospho-Smad 1 (Ser463/465)/ Smad5 (Ser463/465)/ Smad9 (Ser465/467) (Clone D5B10) | Cell Signaling Technologies | Cat# 13820, RRID:AB_2493181 |
| Goat polyclonal anti-GFP | Rockland | Cat# 600-101-215M, RRID:AB_2612804 |
| Rabbit polyclonal anti-RFP/DsRed | MBL International | Cat# PM005, RRID:AB_591279 |
| Deposited Data | ||
| RNA-seq data: Cranial neural crest from Gallus gallus HH9+ dnBMPR1A-FLAG-expressing (replicate 1 and 2) | This paper | https://www.ncbi.nlm.nih.gov/sra/PRJNA717985 |
| RNA-seq data: Cranial neural crest from Gallus gallus HH9+ control (replicate 1 and 2) | (Hutchins et al., 2021) | https://www.ncbi.nlm.nih.gov/bioproject/PRJNA673315 |
| Experimental Models: Organisms/Strains | ||
| Wild type fertilized Gallus gallus eggs | Sunstate Ranch, Sylmar, CA, USA | |
| Oligonucleotides | ||
| Primer: H2B AscI FWD: ATATGGGCGGCCAAGCTTCGAATTGCGCACCA |
This paper | |
| Primer: d2EGFP AscI REV: ATATGGCGCGCCAGAATCTAGAGGCTCGAGAG |
This paper | |
| Primer: BRE AscI FWD: ATATGGCGCGCCCCCTAGAACTATAGTGAGTC |
This paper | |
| Primer: BRE AscI REV: ATATGGCGCGCCCAAGCTCCTTGAATTCGAAT |
This paper | |
| Primer: 2a-RFP FWD 1: CGGGGACGTGGAGGAAAATCCCGGCCCTGAAATGGCCTCCTCCGAGGACG |
This paper | |
| Primer: 2a-RFP FWD 2: CTCCGGCGAGGGCAGGGGAAGTCTTCTAACATGCGGGGACGTGGAGGAAAATCC |
This paper | |
| Primer: 2a-RFP FWD 3 ClaI: AGCTCATCGATGCCGCCACCATGGGCTCCGGCGAGGGCAGGGG |
This paper | |
| Primer: RFP stop REV NotI: ATATGCGGCCGCTTAGGCGCCGGTGGAGTGGCG |
This paper | |
| Primer: BMPR1A ATG XhoI FWD: ATATCTCGAGGCCACCATGACTCGACTGAGAGTTTGTGAGC |
This paper | |
| Primer: dnBMPR1A-FLAG ClaI REV: GCGGCATCGATCTTGTCGTCATCGTCTTTGTAGTCGCCGGAGCCTGCTTCATCTTGTTCCAGGTCACG |
This paper | |
| Recombinant DNA | ||
| Plasmid: BRE::EGFP | (le Dréau et al., 2012) | |
| Plasmid: TCF/Lef::H2B-d2EGFP | (Piacentino et al., 2020) | |
| Plasmid: BRE::H2B-d2EGFP | This paper | |
| Plasmid: pCI H2B-RFP | (Betancur et al., 2010) | |
| Plasmid: pCAG::2a-RFP | This paper | |
| Plasmid: pCAG::dnBMPR1A-FLAG | This paper | |
| Plasmid: pTK-FoxD3-NC1.1m3::GFP | (Simões-Costa et al., 2012) | |
| Software and Algorithms | ||
| Fiji v1.53c | (Schindelin et al., 2012) | https://imagej.net/Fiji |
| Bowtie2 v2.3.5.1 | (Langmead and Salzberg, 2012) | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Cutadapt v2.10 | (Martin, 2011) | https://cutadapt.readthedocs.io/en/stable/ |
| FeatureCounts v2.0.1 | (Liao et al., 2014) | http://subread.sourceforge.net/ |
| R v3.6.1 | (Ihaka and Gentleman, 1996) | https://www.r-project.org/ |
| RStudio v1.2.1335 | (Racine, 2012) | https://www.rstudio.com/ |
| DESeq2 | (Love et al., 2014) | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Python v3.7.6 | (van Rossum and Drake, 2009) | https://www.python.org/downloads/release/python-376/ |
| Pandas v0.24.2 | (McKinney and Team, 2015) | https://pandas.pydata.org/ |
| Bokeh v1.4.0 | (Bokeh Development Team, 2018) | https://docs.bokeh.org/en/latest/index.html |
| Iqplot v0.1.6 | (Bois, 2020) | https://iqplot.github.io/index.html |
| Scipy v1.5.2 | (Virtanen et al., 2020) | https://scipy.org/ |
| Scikit_posthoc v0.6.5 | (Terpilowski, 2019) | https://scikitposthocs.readthedocs.io/en/latest/ |
| Numpy v1.19.2 | (van der Walt et al., 2011) | https://numpy.org/devdocs/index.html |
| Seaborn v0.11.0 | (Waskom, 2012) | https://seaborn.pydata.org/ |
| Holoviews v1.13.3 | (Stevens et al., 2015) | https://holoviews.org/ |