Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Pol II S2P mouse monoclonal antibody | Diagenode | C15200005 |
| Chemicals, peptides, and recombinant proteins | ||
| mApple:PCNA fusion protein | Hadzhiev et al.22 | NA |
| Fluorescently labeled morpholino oligonucleotides | Hadzhiev et al. 22 | NA |
| dCas9 protein | NEB | M0652 |
| dCas9-GFP protein | Novateinbio | PR-137213G |
| Cas9 protein | NEB | M0386M |
| Critical commercial assays | ||
| Genomic DNA Ligation Sequencing Kit | Oxford Nanopore | SQK-LSK110 |
| FISH Tag™ DNA Multicolor Kit | Thermo Fisher | F32951 |
| Click-iT™ RNA Alexa Fluor™ 488 Imaging Kit | Thermo Fisher | C10329 |
| Click-iT™ Nascent RNA Capture Kit | Thermo Fisher | C10365 |
| HiScribe RNA synthesis T7 kit | NEB | E2040 |
| NEBNext® Ultra™ II Directional RNA Library Prep Kit | NEB | E7760S |
| Deposited data | ||
| Oxford Nanopore and PacBio long read sequencing and Nascent RNA capture sequencing | This paper | PRJNA900028 |
| 4-thio-UTP nascent RNA-seq | Heyn P et al.20 | PRJNA207343 |
| CAGE-seq data | Nepal et. al.40 | SRA055273 |
| H3K4me3 and H3K27me3 ChIP-seq | Zhu et al.35 | PRJNA434216 |
| H3K27ac ChIP-seq | Zhang et al.33 | PRJNA473799 |
| ATAC-seq | Liu at al.31 | PRJNA395463 |
| Nanog ChIP-seq | Xu et al.51 | PRJNA156233 |
| Pou5f1 and Sox2 ChIP-seq | Leichsenring et al.27 | PRJNA171706 |
| Experimental models: Organisms/strains | ||
| Zebrafish transgenic line: Tg(Xla.crygc:attP-Gal4vp16, 14UAS:Clover)UoBL1 | This paper | NA |
| Zebrafish transgenic line: Tg(Xla.crygc:attP-Gal4vp16, 14UAS:Clover)UoBL3 | This paper | NA |
| Zebrafish transgenic line: Tg(Xla.crygc:attL-mCherry-miR430-attR-Gal4vp16, 14UAS:Clover)UoBL1 | This paper | NA |
| Zebrafish transgenic line: Tg(Xla.crygc:attL-mCherry-miR430-attR-Gal4vp16, 14UAS:Clover)UoBL3 | This paper | NA |
| Recombinant DNA | ||
| pDB783:Xla.crygc-attP-Gal4vp16-14UAS:Clover | This paper | NA |
| pJET:miR430-attB-mCherry | This paper | NA |
| Software and algorithms | ||
| Canu assembler (v.2.1.1) | Koren et al.37 | https://github.com/marbl/canu/releases |
| ncbi-blast+(v2.11.0) | Altschul et al.38 Camacho et al.39 | https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| purge_dups (v1.2.5) | Guan et al.85 | https://github.com/dfguan/purge_dups |
| RaGOO (v1.1) | Alonge et al.86 | https://github.com/malonge/RaGOO |
| segemehl aligner (v0.3.4) | Otto et al.93 | https://www.bioinf.uni-leipzig.de/Software/segemehl/ |
| bowtie (v1.2.3) | Langmead et al.89 | https://github.com/BenLangmead/bowtie/releases |
| CAGEr (v1.18) | Haberle et al.90 | https://doi.org/doi:10.18129/B9.bioc.CAGEr |
| STAR (v2.7.3a) | Dobin et.al.94 | https://github.com/alexdobin/STAR/ |
| cluster-buster | Frith et al.52 | https://github.com/weng-lab/cluster-buster/ |
| DESeq2 (v1.36.0) | Love et al.103 | https://doi.org/doi:10.18129/B9.bioc.DESeq2 |
| ClusterScan(v0.2.2) | Volpe et al.91 | https://github.com/pyrevo/ClusterScan |
| karyoploteR (v1.18.0) | Gel et al.92 | https://doi.org/doi:10.18129/B9.bioc.karyoploteR |
| SeqPlots(v1.27) | Stempor et al.95 | https://doi.org/doi:10.18129/B9.bioc.seqplots http://przemol.github.io/seqplots/ |
| DiffLogo | Nettling et al.96 | https://doi.org/doi:10.18129/B9.bioc.DiffLogo |
| ggseqlogo | Wagih,O.97 | https://github.com/omarwagih/ggseqlogo |