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. Author manuscript; available in PMC: 2023 Mar 3.
Published in final edited form as: Mol Cell. 2022 Feb 18;82(5):986–1002.e9. doi: 10.1016/j.molcel.2022.01.024

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Mouse monoclonal anti-GFP Thermo Fisher Scientific Cat#A-11120; RRID:AB_221568
Goat anti-mouse secondary antibody, Alexa Fluor Plus 488 Thermo Fisher Scientific Cat#A32723; RRID:AB_2633275
Goat Anti-Rabbit IgG H&L (HRP) Abcam Cat#ab6721 RRID:AB_955447
Rabbit polyclonal anti-H3K27ac Abcam Cat#ab4729; RRID:AB_2118291
Rabbit polyclonal anti-H2A.Z Abcam Cat#ab4174; RRID:AB_304345
Rabbit polyclonal anti-H2BK15ac Diagenode Cat#C15410220
Rabbit polyclonal anti-H2AK5ac Diagenode Cat#C15410215;
Rabbit monoclonal anti-BRD4 Cell Signaling Technology Cat#13440; RRID:AB_2687578
Rabbit monoclonal anti-H2A.Z(Lys4/Lys7)ac Cell Signaling Technology Cat#75336, RRID:AB_2799867
Rabbit monoclonal anti-H2BK5ac Cell Signaling Technology Cat#12799; RRID:AB_2636805
Rabbit monoclonal anti-H3K14ac Cell Signaling Technology Cat#7627; RRID:AB_10839410
Rabbit monoclonal anti-H3K36ac Cell Signaling Technology Cat#27683; RRID:AB_2798946
Rabbit monoclonal anti-H4K16ac Cell Signaling Technology Cat#13534; RRID:AB_2687581
Rabbit polyclonal anti-H3K9ac Active Motif Cat#39137; RRID:AB_2561017
Rabbit polyclonal anti-H3K18ac Abcam Cat#ab1191; AB_298692
Rabbit polyclonal anti-H4K8ac Abcam Cat#ab15823; RRID:AB_880455
Rabbit polyclonal anti-H3K4me3 Abcam Cat#ab8580 RRID:AB_306649
Rabbit polyclonal anti-H3K4me1 Diagenode Cat#C15310037
Mouse monoclonal anti-Pol II [8WG16] Abcam Cat#ab817; RRID:AB_306327
Mouse monoclonal anti-Pol II [8WG16] BioLegend Cat#664912; RRID:AB_2650945
Goat polyclonal anti-Myc tag Abcam Cat#ab9132; RRID:AB_307033
Goat anti-rabbit-IgG-Atto647N Sigma-Aldrich Cat#40839; RRID:AB_1137669
Rabbit polyclonal anti-Actin Sigma-Aldrich Cat#A5060; RRID:AB_476738
Mouse monoclonal anti-FLAG Sigma-Aldrich Cat#F3165; RRID:AB_259529
Rabbit polyclonal anti-p300a This paper N/A
Rabbit polyclonal anti-Nfya Charles Sagerström lab N/A
Rabbit polyclonal anti-Eomesa Fiona Wardle lab N/A
Rabbit polyclonal anti-Brd4 Dawid lab N/A
Chemicals, Peptides, and Recombinant Proteins
α-amanitin Sigma-Aldrich Cat#A2263
Triptolide Sigma-Aldrich Cat#T3652
Flavopiridol hydrochloride hydrate Sigma-Aldrich Cat# F3055
Critical Commercial Assays
ChIP DNA Clean & Concentrator Kits ZYMO RESEARCH Cat#D5205
Nextera DNA Library Prep Kit Illumina Cat#FC-121–1030
Click-iT™ RNA Alexa Fluor™ 594 Imaging Kit Thermo Fisher Scientific Cat#C10330
Click-iT™ Nascent RNA Capture Kit Thermo Fisher Scientific Cat#C10365
SuperScript™ VILO™ cDNA Synthesis Kit Thermo Fisher Scientific Cat#11754–050
MAXIscript™ SP6 Transcription Kit Thermo Fisher Scientific Cat#AM1308
mMESSAGE mMACHINE™ T3 Transcription Kit Thermo Fisher Scientific Cat#AM1348
mMESSAGE mMACHINE™ SP6 Transcription Kit Thermo Fisher Scientific Cat#AM1340
AmpliScribe™ T7-Flash™ Transcription Kit Lucigen Cat#ASF3257
Deposited Data
Datasets for Omni-ATAC seq, ChIP-seq, Click-iT-seq, RNA-seq, CUT&TAG in WT and MZnps embryos This paper SRP355652
Nanog ChIP-seq datasets Xu et al., 2012 GSE34683
ATAC-seq datasets at oblong and sphere stages Pálfy et al., 2020 GSE130944
ATAC-seq datasets at oblong and dome stages Liu et al., 2018 GSE101779
CAGE datasets at high/oblong/sphere/shield stages Nepal et al., 2013 SRA055273
Ribosome profiling datasets at 2 hpf Bazzini et al., 2014 GSE53693
Experimental Models: Organisms/Strains
Zebrafish: MZnps, triple maternal-zygotic mutant for nanog−/−;pou5f3−/−;sox19b−/− This paper N/A
Zebrafish: TU-AB, and TL strains N/A N/A
Oligonucleotides (See Table S1 for oligonucleotides used)
Recombinant DNA
pT3TS-zdCas9–3XGFP Chan et al., 2019 N/A
pcDNA-dCas9-p300 Core Hilton et al., 2015 Addgene Plasmid #61357; RRID:Addgene_61357
pT3TS-dCas9-HAT This paper N/A
pT3TS-dCas9-dHAT This paper N/A
pCS2+nanog Lee et al., 2013 N/A
pCS2+pou5f3 Lee et al., 2013 N/A
pCS2+pou5f3–6Xmyc This paper N/A
pCS2+sox19b-6Xmyc This paper N/A
Software and Algorithms
Bowtie2 Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2
Skewer Jiang et al., 2014 https://github.com/relipmoc/skewer
STAR Dobin et al., 2012 https://github.com/alexdobin/STAR
SAMtools Li et al., 2009 http://www.htslib.org
BEDTools Quinlan et al., 2010 https://bedtools.readthedocs.io/en/latest/
MACS2 Zhang et al., 2008 https://github.com/taoliu/MACS
DESeq2 Love et al., 2014 https://bioconductor.org/packages/release/bioc/ht ml/DESeq2.html
MEME suite Bailey et al., 2009 http://meme-suite.org
Nucleosome occupancy prediction model Kaplan et al. 2009 https://github.com/KaplanLab/NucleosomeModel
Python Python 3.8 https://www.python.org
R R 3.6.2 https://www.r-project.org
GeneAbacus Charles E. Vejnar https://github.com/vejnar/geneabacus
FONtools Charles E. Vejnar https://github.com/vejnar/fontools
LabxDB seq Vejnar et al., 2020 https://gitlab.com/vejnar/labxdb