KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| p-Histone H3 Antibody (Ser 10) | Santa Cruz | Cat# sc-8656-R; RRID: AB_653256 |
| GFP Monoclonal Antibody (3E6) | Invitrogen | Cat# A-11120; RRID: AB_221568 |
| Bacterial and Virus Strains | ||
| One Shot TOP10 Chemically Competent E. coli | Invitrogen | Cat# C404006 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| 5-Aza-2_-deoxycytidine | Sigma | A3656-5MG |
| IWR-1 | Enzo Life Sciences | BML-WN103-0005 |
| TRIM(1-[2-(Trifluoromethyl)phenyl]imidazole) | Sigma | T7313-100MG |
| SB431542 | Stemgent | 04-0010-10 |
| Coming Collagen I | Fisher | 354249 |
| Critical Commercial Assays | ||
| mMESSAGE mMACHINE | Invitrogen | AM1340 |
| RNeasy Mini kit | QIAGEN | 74106 |
| RNeasy Micro kit | QIAGEN | 74004 |
| LightCycler 480 Sybr Green master mix | Roche | 04-887-352-001 |
| Ovation RNA-Seq System V2 | Nugen | N/A |
| TruSeq RNA Library Prep Kit v2 | Illumina | RS-122-2001 |
| DNeasy Blood & Tissue Kits | QIAGEN | 69506 |
| EZ DNA Methylation-Direct kit | Zymo Research | D5021 |
| Deposited Data | ||
| Raw and analyzed data | This paper | GSE121991 |
| Histone datasets | Bogdanovic et al., 2012 | GSE32483 |
| Zebrafish GRCz10 reference genome | Genome Reference Consortium | https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.5/ |
| Zebrafish danRer7 reference genomes | Wellcome Trust Sanger Institute | https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.4/ |
| Experimental Models: zebrafish Strains | ||
| tet2mk17/mk17, tet3mk18/mk18 double-mutant tet2/3DM) | Li etal., 2015 | N/A |
| Tg(myl7:EGFP) | Huang et al., 2003 | N/A |
| Tg(tcf21:NLS-EGFP) | Kikuchi et al., 2011w | N/A |
| Tg (tcf21:DsRed2) | Kikuchi et al., 2011 | N/A |
| Tg(7xTCF-Xla.Siam:GFP)ia4 | Moro et al., 2012 | N/A |
| Tg(kdrl:EGFP-NLS) | Zygmunt et al., 2011 | N/A |
| Tg(tp1:EGFP) | Parsons et al., 2009 | N/A |
| Oligonucleotides | ||
| Splice-blocking MO (5′ TGC AGT AAT TTA CCG GAG TGT TCT C 3′) for sox9b | Yan et al., 2005 | N/A |
| PCR primer sequences, see Table S1 | This paper | N/A |
| Recombinant DNA | ||
| Plasmid: pEF1/V5-His-hTET2 | Li etal., 2015 | N/A |
| Plasmid: pEF1/V5-His-mutant hTET2 | Li etal., 2015 | N/A |
| Plasmid: pCS2+-inhbaa | This paper | N/A |
| Plasmid: pCS2+-sox9b | This paper | N/A |
| Plasmid: pCS2+-has2 | This paper | N/A |
| Software and Algorithms | ||
| SPOT advanced imaging software | SPOT Imaging | N/A |
| Zen software | ZEISS | N/A |
| macs14 1.4.2 | Shirley Liu lab | http://liulab.dfci.harvard.edu/MACS/00README.html |
| Lasergene | DNASTAR | N/A |
| Prism 7 | GraDhDad | N/A |