Reagent/Resource	Reference or Source	Identifier or Catalog Number
Experimental Models
HT115 (E. coli)	Caenorhabditis Genetics Center	N/A
OP50 (E. coli)	Caenorhabditis Genetics Center	N/A
N2 Bristol (C. elegans)	Caenorhabditis Genetics Center	N/A
NR350 (C. elegans)	Caenorhabditis Genetics Center	N/A
RW1596 (C. elegans)	Caenorhabditis Genetics Center	N/A
SJ4144 (C. elegans)	Caenorhabditis Genetics Center	N/A
TU3310 (C. elegans)	Caenorhabditis Genetics Center	N/A
VP303 (C. elegans)	Caenorhabditis Genetics Center	N/A
SYD0600 (C. elegans)	This study	N/A
SYD0848 (C. elegans)	This study	N/A
SYD1115 (C. elegans)	This study	N/A
CB1370 (C. elegans)	Caenorhabditis Genetics Center	N/A
DA465 (C. elegans)	Caenorhabditis Genetics Center	N/A
SYD1299 (C. elegans)	This study	N/A
SYD1303 (C. elegans)	This study	N/A
SYD1315 (C. elegans)	This study	N/A
SYD1317 (C. elegans)	This study	N/A
SYD1325 (C. elegans)	This study	N/A
Recombinant DNA
coel::RFP	Addgene	Cat # 8938
semo‐1p::gfp	This study	N/A
egl‐17p::Myri‐mCherry	Guangshuo Ou Lab, Tsinghua University	N/A
irx‐1p::gfp	This study	N/A
myrf‐2p::gfp	This study	N/A
Antibodies
NA in this study
Oligonucleotides and other sequence‐based reagents
Sequences of oligonucleotides	This study	Table 2
Chemicals, Enzymes and other reagents
AMPure XP	Beckman Coulter	Cat # A63881
RNeasy Mini	QIAGEN	Cat # 74104
NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina	New England Biolabs	Cat # E7420L
Betaine	Sigma‐Aldrich	Cat # 61962
Betaine solution	Sigma‐Aldrich	Cat# B0300‐1VL
Collagenase, Type 4	Worthington Biochemical Corporation	Cat# LS004188
DTT	ABCOne	Cat# D85571‐5g
FUdR	Adamas	Cat# 61000B
IPTG, Dioxane Free	GBCBIO Technologies Inc.	Cat# 1758‐1700‐100g
KAPA HiFi HotStart ReadyMix	KAPA Biosystems	Cat # KK2601
KOD ‐Plus‐ Neo	TOYOBA	Cat # KOD‐401
NovoStart® SYBR qPCR SuperMix Plus	Novoprotein	Cat# E096
PrimeScript™ RT reagent Kit (Perfect Real Time)	Takara	Cat# RR037A
Protease from Streptomyces griseus	Sigma‐Aldrich	Cat# P6911
ProtoScript II Reverse Transcriptase	New England Biolabs	Cat # M0368L
Q5® High‐Fidelity DNA Polymerase	New England Biolabs	Cat# M0491L
RiboLock RNase Inhibitor	Thermo Fisher	Cat # EO0381
RNaseOUT™ Recombinant Ribonuclease Inhibitor	Invitrogen	Cat# 10777019
Sodium citrate dihydrate	Shanghai Experment Reagent	Cat# 174000AR
Tn5	Picelli et al (2014)
TRIzol™ Reagent	Invitrogen	Cat# 15596018
Software
ARACNe‐AP	Lachmann et al (2016)
Cytoscape v3.8.2	http://www.cytoscape.org
featureCounts	Liao et al (2014)
GraphPad Prism 8	https://www.graphpad.com/
MARINa	Aytes et al (2014)
scikit‐learn v0.24.2	http://scikit‐learn.org/
STAR v2.6.0c	Dobin et al (2013)
TBtools	Chen et al (2020)
Fiji	https://imagej.net/imagej‐wiki‐static/Fiji
Other
2200 TapeStation system	Agilent
Agilent D1000 ScreenTape	Agilent
Agilent High Sensitivity D5000 ScreenTape	Agilent
Agilent High Sensitivity RNA ScreenTape	Agilent
Illumina HiSeq X Ten	Illumina
Illumina NovaSeq 6000	Illumina
Illumina HiSeq2500	Illumina
The Qubit 2.0 Fluorometer	Thermo Fisher
Nikon D4 camera with a Nikon AF Zoom‐Nikkor 24–85 mm lens	Nikon
Olympus SZX16 stereo microscope	Olympus
Olympus BX53 microscope	Olympus
Olympus IXplore SpinSR microscope	Olympus