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
|