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. Author manuscript; available in PMC: 2023 Oct 23.
Published in final edited form as: Dev Cell. 2023 Aug 8;58(19):1898–1916.e9. doi: 10.1016/j.devcel.2023.07.007

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Rabbit polyclonal anti-Zelda Koenecke et al.108 366735–1
Rabbit polyclonal anti-Bicoid This paper U9982EL040–1
Rabbit polyclonal anti-Caudal This paper U4197EL190–1
Rabbit polyclonal anti-Dorsal He et al.58 126740–44
Rabbit polyclonal anti-Twist He et al.58 131424–2
Rabbit polyclonal anti-GAF This paper 163185–42
Rabbit polyclonal anti-H3K27ac Active Motif 39133; RRID: AB_2561016
Mouse monoclonal anti-H3K4me1 Active Motif 39635; RRID: AB_2793284
Anti-rabbit IgG Alexa Fluor 568 secondary antibody ThermoFisher A10042; RRID: AB_2534017
Chemicals, peptides, and recombinant proteins
37% formaldehyde solution VWR Cat# 50–00-0
Dynabeads Protein A ThermoFisher Cat# 10008D
phi29 DNA polymerase New England Biolabs Cat# M0269S
Lambda exonuclease New England Biolabs Cat# M0262S
Q5 High-Fidelity 2x Master Mix New England Biolabs Cat# M0492S
dNTP solution mix New England Biolabs Cat# N0447S
MNase New England Biolabs Cat# M0247S
RNase A ThermoFisher Cat# EN0531
Phenol:chloroform:isoamyl alcohol (25:24:1) (v/v/v) VWR Cat# 136112–00-0
Proteinase K ThermoFisher Cat# 25530049
Western Blocking Reagent Millipore Sigma Cat# 11921681001
ProLong Gold Antifade Mountant with DAPI ThermoFisher Cat# P36931
OptiPrep Density Gradient Medium Millipore Sigma Cat# D1556
ProLong Glass Antifade Mountant ThermoFisher Cat# P36980
Critical commercial assays
End Repair Module New England Biolabs Cat# E6050S
dA-Tailing Module New England Biolabs Cat# E6053S
Quick Ligation Kit New England Biolabs Cat# M2200S
High Throughput Library Prep Kit KAPA Biosystems Cat# KK8234
Monarch DNA Gel Extraction Kit New England Biolabs Cat# T1020
Monarch PCR & DNA Cleanup Kit New England Biolabs Cat# T1030
PURExpress In Vitro Protein Synthesis Kit New England Biolabs Cat# E6800
Hybridization Chain Reaction (HCR) v3.0 Molecular Instruments N/A
Deposited data
Raw and analyzed NGS and PBM data This paper GEO: GSE218852
Trained deep learning models (Zenodo) This paper Zenodo: https://zenodo.org/recore/8075860 https://doi.org/10.5281/zenodo.8118135
Raw images This paper ODR: http://www.stowers.org/research/publications/libpb-2357
Experimental models: Organisms/strains
Drosophila melanogaster: Oregon-R Koenecke et al.108 FlyBase: FBsn0000276
Drosophila melanogaster: UAS-shRNA-zld: P{UAS-zld.shRNA} Sun et al.6 FlyBase: FBtp0147479
Drosophila melanogaster: Maternal Triple Driver (MTD)-Gal4: P{COG-GAL4:VP16}; P{Gal4-nos.NGT}40; P{nos-Gal4-VP16} Bloomington Stock Center BSC: 31777
Drosophila melanogaster: gd7: gd7/winscy, P{hs-hid}5 Koenecke et al.108 N/A
Drosophila melanogaster: cic6: cic6/TM3, Sb1 Papagianni et al.101 N/A
Oligonucleotides
Oligonucleotides for ChIP-nexus, see Table S2 IDT https://research.stowers.org/zeitlingerlab/protocols.html
Illumina Index primer 1: 5’-CAAGCAGAAGAC GGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3’ IDT https://support-docs.illumina.com/SHARE/AdapterSeq/1000000002694_17_illumina_adapter_sequences.pdf
Illumina Index primer 2: 5’-AATGATACGGCGACC ACCGAGATCTACAC[i5]TCGTCGGCAGCGTC-3’ IDT https://support-docs.illumina.com/SHARE/AdapterSeq/1000000002694_17_illumina_adapter_sequences.pdf
Illumina Transposase adapter read 1 (Nextera A): 5’- TCGTCGGCAGCGTCAGATGTGTATAA GAGACAG-3’ IDT https://support-docs.illumina.com/SHARE/AdapterSeq/1000000002694_17_illumina_adapter_sequences.pdf
Illumina Transposase adapter read 2 (Nextera B): 5’- GTCTCGTGGGCTCGGAGATGTGTATA AGAGACAG-3’ IDT https://support-docs.illumina.com/SHARE/AdapterSeq/1000000002694_17_illumina_adapter_sequences.pdf
Mosaic end primer: /5Phos/CTGTCTCTTATAC A/3ddC/ IDT Tn5mC1.1-A1block
gd7 heat shock forward primer: 5’-GGAGCGAC AATTCAATTCAAACAAGC-3’ IDT N/A
gd7 heat shock reverse primer: 5’-GTAGCTGTG GCTGCAGTGCATCG-3’ IDT N/A
Recombinant DNA
pETM11-Sumo3-Tn5 plasmid Hennig et al.148 E54K,L372P
His6-tagged SenP2 protease plasmid Hennig et al.148 N/A
Software and algorithms
FIJI Schindelin et al.149 https://fiji.sc/
Cutadapt v.2.5 Martin154 https://cutadapt.readthedocs.io/en/v2.5/
Bowtie2 v.2.3.5.1 Langmead and Salzberg155 https://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
MACS2 v.2.2.7.1 Zhang et al.156 https://github.com/macs3-project/MACS
Irreproducible Discovery Rate framework v.2.0.3 Li et al.157 https://github.com/nboley/idr
Picard v.2.23.8 Broad Institute of MIT and Harvard158 http://broadinstitute.github.io/picard
deepTools2 v.3.5.1 Ramírez et al.159 https://deeptools.readthedocs.io/en/latest/
BPNet software Avsec et al.59 https://github.com/kundajelab/bpnet/
Keras v.2.2.4 & v.2.5.0 Chollet et al.160 https://pypi.org/project/keras/
TensorFlow1 backend v.1.7 & v.2.5.1 Abadi et al.161 https://www.tensorflow.org/install/pip
Adam optimizer Kingma and Ba162 N/A
DeepLIFT v.0.6.9.0 Shrikumar et al.163 https://github.com/kundajelab/DeepExplain
TF-MoDISco v.0.5.3.0 & v.0.5.16.0 Shrikumar et al.164 https://github.com/kundajelab/tfmodisco
ChromBPNet software Anshul Kundaje’s lab, Stanford University https://github.com/kundajelab/chrombpnet
DeepLIFT v.0.6.13.0 Shrikumar et al.163 https://github.com/kundajelab/shap
DESeq2 v.1.36.0 Love et al.109 https://bioconductor.org/packages/release/bioc/html/DESeq2.html
R v.4.2.0 R core team https://www.r-project.org/
Rstudio RStudio https://rstudio.com
ggplot2 v.3.3.6 Wickham168 https://ggplot2.tidyverse.org/
Other
All code and analyses that contributed to this work This paper https://github.com/zeitlingerlab/Brennan_Zelda_2023 https://doi.org/10.5281/zenodo.8118135
Bioruptor Pico sonication device Diagenode https://www.diagenode.com/en/p/bioruptor-pico-sonication-device
Point scanning confocal microscope Zeiss 780
Spinning disk microscope Nikon Eclipse Ti2