REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal anti-GFP	Abcam	Cat# ab290; RRID: AB_303395
Bacterial and Virus Strains
Escherichia coli: HB101 Strain	CGC	HB101
Escherichia coli: HT115 Strain	CGC	HT115
Escherichia coli: OP50 Strain	CGC	OP50
Chemicals, Peptides, and Recombinant Proteins
Chitinase	Sigma	Cat# C6137
cOmplete™, Mini Protease Inhibitor Cocktail	Roche	Cat# 11836153001
Dextran sulfate sodium salt	Sigma	Cat# D6001
EvaGreen® Dye	Biotium	Cat# 31000
Formaldehyde solution	Sigma	Cat# F8775
Formamide (Deionized)	Ambion	Cat# AM9342
Leibovitz;s L-15 Medium, no phenol red	Gibco	Cat# 21083027
Penicillin-Streptomycin	Sigma	Cat# P4458
ProLong™ Gold Antifade reagent with DAPI	Invitrogen	Cat# P36935
Pronase	Sigma	Cat# P6911
SYBR™ Green I Nucleic Acid Gel Stain	ThermoFisher	Cat# S7563
SYTOX™ AADvanced Dead Cell Stain Kit	Invitrogen	Cat# S10349
Critical Commercial Assays
AMPure XP Beads	Beckman Coulter	Cat# A63882
DNA Clean & Concentrator Kit-5	Zymo Research	Cat# D4013
Dynabeads™ Protein A Immunoprecipitation Kit	ThermoFisher	Cat# 100006D
NEBNext® High Fidelity 2x PCR Master Mix	New England BioLabs	Cat# M0541L
NEBNext® Ultra II DNA Library Prep Kit for Illumina®	New England BioLabs	Cat# E7645S
Nextera DNA Library Prep Kit	Illumina	Cat# 15028212
Nextera i7 and i5 adapters	Illumina	Cat# 20027213
Protein Assay Dye Reagent Concentrate	Bio-Rad	Cat# 5000006
Quasar 670-conjugated RNA FISH Probe Sets	Biosearch Technologies	N/A
Deposited Data
ATAC-seq & ChIP-seq data	This Study	GEO: GSE155392
Experimental Models: Organisms/Strains
Please see Table S4 for a complete list of strains used in this study
Oligonucleotides
crRNA targeting che-1 #1: TAAAGAGGGTGGAGCTTCAG	IDT	N/A
crRNA targeting che-1 #2: CACAGAGTGGGAACTTGCAT	IDT	N/A
crRNA targeting lsy-6 #1: ATGAGACGCATTTCGATGAC	IDT	N/A
crRNA targeting tbx-37 #1: GCTCAAAATTACAATAATTT	IDT	N/A
crRNA targeting tbx-37 #2: GAGCAGCAAACTGTGGCTGG	IDT	N/A
crRNA targeting tbx-38 #1: ATTGTACTGCACTGATCTCC	IDT	N/A
crRNA targeting tbx-38 #2: TACCTATTGCCTTTCTCCCC	IDT	N/A
crRNA targeting tbx-11 #1: AACAGGAAAAATACACCCGG	IDT	N/A
crRNA targeting tbx-11 #2: CCGCCCAACACGTGGCAAGG	IDT	N/A
crRNA targeting tbx-43 #1: ATTTTTCCATAAGCGCCACG	IDT	N/A
crRNA targeting tbx-43 #2: GGCCGAGAACTCCTCCAACG	IDT	N/A
Recombinant DNA
Please see Table S5 for a complete list of Recombinant DNA used in this study
Software and Algorithms
bowtie2 (v2.2.4)	Langmead and Salzberg, 2012	N/A
ChIPseeker (v1.22.1)	Yu et al., 2015	N/A
Cutadapt (v1.18)	Martin, 2011	N/A
GenomicRanges (v1.38.0)	Lawrence et al., 2013	N/A
ImageJ (Fiji)	NIH	N/A
kent-uscs (v2.79)	Kent et al., 2010	N/A
macs2 (v2.1.0)	Zhang et al., 2008	N/A
MEME Suite (v5.1.1)	Machanick & Bailey, 2011	N/A
MetaMorph	Molecular Devices	N/A
rtracklayer (v1.46.0)	Lawrence et al., 2009	N/A
Picard-tools (v2.18.27)	Broad Institute	N/A
Prism 7	GraphPad Prism	N/A
Rsubread (v2.0.1)	Liao et al., 2019	N/A
SAMtools (v0.1.18)	Li et al., 2009	N/A
SciPy	Virtanen et al., 2020	N/A
SIMI BioCell	Schnabel et al., 1997	N/A
Time to Live	Caenotec	N/A
Zen	Zeiss	N/A
Other
Axio Imager.Z2	Zeiss	N/A
Axio Observer Confocal with Airyscan	Zeiss	Cat# LSM880
Bioruptor® Plus sonication device	Diagenode	Cat# B01020001
HiSeq 2500 Sequencing System	Illumina	N/A
NanoDrop™ 3300 Fluorospectrometer	ThermoFisher	Cat# ND-3300
pluriStrainer® 5 μm cell strainer	pluriSelect	Cat# 43-10005-40
SH800S Cell Sorter	Sony	N/A
Sorting Chip 100 μm	Sony	Cat# LE-C3210
Visiscope Spinning Disc Confocal	Visitron Systems GmbH	N/A