KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-Pol II 8WG16, ascites | Bio-Legend | MMS-126R |
| Mouse monoclonal anti-Flag | Sigma-Aldrich | Cat#F3165 |
| Rabbit polyclonal anti-Vegt | Sudou et al., 2012 | N/A |
| Rabbit polyclonal anti-Foxh1 | Chiu et al., 2014 | N/A |
| Rabbit polyclonal anti-Otx1, designed against the peptide sequence GYTGTGLPFNSSDC (AA 288–101 of the Xenopus tropicalis Otx1 protein) | GenScript; This Paper | N/A |
| Rabbit polyclonal anti-H3K4me1 | Abcam | Cat#ab8895 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Dynabeads Protein G | Life Technologies | Cat#10003D |
| Critical Commercial Assays | ||
| mMessage mMachine Sp6 Transcription Kit | Thermo Fisher Scientific | Cat#AM1340 |
| SYBR Green I Master | Roche | Cat#04707516001 |
| NEXTflex ChIP-seq kit | Bioo Scientific | Cat#NOVA-5143–01 |
| Superscript II | Life Technologies | Cat#18064014 |
| KAPA HiFi HotStart ReadyMix (2x) | Kapa Biosystems | Cat#KK2601 |
| Agencourt AMPure XP beads | Beckman Coulter | Cat#A63881 |
| Nextera DNA Library Prep Kit | Illumina | Cat#FC-121–1030 |
| TURBO DNase | Thermo Fisher | Cat#AM2238 |
| Deposited Data | ||
| X. tropicalis RNA-seq and ChIP-seq | This Paper | GEO:GSE118024 |
| X. tropicalis genome version 9.0 | Hellsten et al., 2010; Karimi et al., 2018 | RRID:SCR_003280; URL: http://www.xenbase.org/entry/ |
| X. tropicalis gastrula stage (Stage 10.5) dissected fragments, RNA-seq | Blitz et al., 2017 | GEO:GSE81458 |
| X. tropicalis wild type embryo temporal profiling, RNA-seq | Owens et al., 2016 | GEO:GSE65785 |
| X. tropicalis Stage 8 ChIP-seq input DNA | Charney et al., 2017a | GEO:GSE85273 |
| X. tropicalis Foxh1 Stage 8, ChIP-seq | Charney et al., 2017a | GEO:GSE85273 |
| X. tropicalis Pol II Stage 7–10, ChIP-seq | Charney et al., 2017a | GEO:GSE85273 |
| X. tropicalis Foxa Stage 10, ChIP-seq | Charney et al., 2017a | GEO:GSE85273 |
| X. tropicalis H3K9me2 Stage 9–30, ChIP-seq | Hontelez et al., 2015 | GEO:GSE67974 |
| X. tropicalis H4K20me3 Stage 9–30, ChIP-seq | Hontelez et al., 2015 | GEO:GSE67974 |
| X. tropicalis H3K4me1 Stage 9–30, ChIP-seq | Hontelez et al., 2015 | GEO:GSE67974 |
| X. tropicalis Ep300 Stage 8–30, ChIP-seq | Hontelez et al., 2015 | GEO:GSE67974 |
| X. tropicalis H3K4me3 Stage 8–30, ChIP-seq | Hontelez et al., 2015 | GEO:GSE67974 |
| X. tropicalis H3K4me1 Stage 8–10, ChIP-seq | Gupta et al., 2014 | GEO:GSE56000 |
| X. tropicalis H3K27ac Stage 8–10, ChIP-seq | Gupta et al., 2014 | GEO:GSE56000 |
| X. tropicalis Ctnnb1 Stage 10, ChIP-seq | Nakamura et al., 2016 | GEO:GSE72657 |
| X. tropicalis Smad2/3 Stage 10, ChIP-seq | Chiu et al., 2014 | GEO:GSE53654 |
| X. tropicalis Gsc Stage 10, ChIP-seq | Yasuoka et al., 2014 | DRA:DRA000576; DRA000577 |
| X. tropicalis Otx2 Stage 10, ChIP-seq | Yasuoka et al., 2014 | DRA:DRA000508; DRA000510 |
| X. tropicalis Jarid Stage 9, ChIP-seq | van Heeringen et al., 2014 | GEO:GSE41161 |
| X. tropicalis Ezh2 Stage 9, ChIP-seq | van Heeringen et al., 2014 | GEO:GSE41161 |
| X. tropicalis Foxh1 MO, RNA-seq | Chiu et al., 2014 | GEO:GSE53654 |
| Experimental Models: Organisms/Strains | ||
| X. tropicalis, out-bred Nigerian | University of Virginia, NASCO | URL: https://www.enasco.com/ |
| Oligonucleotides | ||
| Template switching oligo | Picelli et al., 2014 | N/A |
| ISPCR primers | Picelli et al., 2014 | N/A |
| Indexing primers | Buenrostro et al., 2013 | N/A |
| Primers for RT-qPCR and ChIP-qPCR (See Table S5) | Integrated DNA Technologies | N/A |
| Otx1 MO 5′- ATGACATCATGCTCAAGGCTGGACA-3′ | GeneTools; This Paper | N/A |
| Vegt MO 5′-TGTGTTCCTGACAGCAGTTTCTCAT-3′ | GeneTools; Rana et al., 2006 | N/A |
| Foxh1 MO 5′-TCATCCTGAGGCTCCGCCCTCTCTA-3′ | GeneTools; Chiu et al., 2014 | N/A |
| Recombinant DNA | ||
| pCS2+otx1 (X. tropicalis otx1 ORF) | This paper | N/A |
| pCS2+vegt (X. tropicalis vegt ORF) | This paper | N/A |
| pCS2+3xFLAG-otx1 (X. tropicalis otx1 ORF) | This paper | N/A |
| Software and Algorithms | ||
| RSEM v.1.2.12 | Li and Dewey, 2011 | RRID:SCR_013027; URL: http://deweylab.biostat.wisc.edu/rsem/ |
| Bowtie 2 v2.2.7 | Langmead and Salzberg, 2012 | RRID:SCR_016368; URL: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| EBseq v1.8.0 | Leng et al., 2013 | RRID:SCR_003526;URL: https://www.biostat.wisc.edu/~kendzior/EBSEQ/ |
| R v3.1.0 | R Core Team, 2014 | RRID:SCR_001905; URL:http://www.r-project.org/ |
| MACS2 v2.0.10 | Zhang et al., 2008 | RRID:SCR_013291;URL: https://github.com/taoliu/MACS |
| Irreproducibility Discovery Rate | Li et al., 2011 | URL: https://sites.google.com/site/anshulkundaje/projects/idr |
| HOMER v4.7 | Heinz et al., 2010 | RRID:SCR_010881;URL: http://homer.ucsd.edu/homer/ |
| DREME | Bailey, 2011 | RRID:SCR_001783; URL: http://meme-suite.org/ |
| TOMTOM | Gupta et al., 2007 | RRID:SCR_001783; URL: http://meme-suite.org/ |
| Samtools v0.1.19 | Li et al., 2009 | RRID:SCR_002105; URL: http://samtools.sourceforge.net/ |
| Bedtools v2.19.1 | Quinlan and Hall, 2010 | RRID:SCR_006646; URL: https://github.com/arq5x/bedtools2 |
| IGV v2.3.20 | Robinson et al., 2011 | RRID:SCR_011793; URL: http://software.broadinstitute.org/software/igv/ |
| Sratoolkit v2.8.1 | NCBI NIH | URL: https://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/ |
| Gene Ontology | Ashburner et al., 2000; The Gene Ontology Consortium, 2017 | RRID:SCR_002143;URL: http://geneontology.org/ |
| Rank Ordering of Super-Enhancers (ROSE) | Lové n et al., 2013; Whyte et al., 2013 | URL: http://younglab.wi.mit.edu/super_enhancer_code.html |