Skip to main content
. Author manuscript; available in PMC: 2023 Apr 25.
Published in final edited form as: Curr Biol. 2022 Mar 7;32(8):1715–1727.e8. doi: 10.1016/j.cub.2022.02.040

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Mouse monoclonal anti-FLAG M2 Sigma-Aldrich Cat# F1804
Bacterial and virus strains
E. coli Caenorhabditis Genetics Center (CGC) WormBase: OP50; WormBase: WBStrain00041969
Chemicals, peptides, and recombinant proteins
Aldicarb ChemService Cat# N-11044-100MG
Sodium Azide Sigma-Aldrich Cat# 71289
RNase-free DMF Acros Organics Cat# AC327175000
OptiPrep Cosmo Bio USA Cat # AXS-1114542
Dynabeads Protein G Thermo Fisher Cat# 10003D
Dynabeads M-270 Carboxylic Acid Thermo Fisher Cat# 14305D
Alt-R S.p. Cas9 Nuclease V3 IDT Cat# 1081059
Alt-R CRISPR-Cas9 tracrRNA IDT Cat# 1072533
Critical commercial assays
NucleoSpin Tissue XS Takara Cat# 740901.250
Universal RNA-seq with NuQauant Tecan Cat# 0533-32
Deposited data
Raw and analyzed RNA-seq data This paper GEO: #GSE188489
CEH-48 ChIP-seq dataset 17 https://www.encodeproject.org/; Experiment: ENCSR844VCY
CEH-38 ChIP-seq dataset 17 http://www.modencode.org/; Accession # modEncode_4800
Experimental models: Organisms/strains
C. elegans: Strain N2 Caenorhabditis Genetics Center (CGC) WormBase: N2; WormBase: WBStrain00000001
ceh-38(tm321) II 20 FX00321
ceh-48(tm6112) IV 20 FX06112
rab-3(js49) 19 NM791
otIs356(rab-3prom1::2xNLS-tagRFP) V 3 OH10690
otIs381(ric-19prom6::2xNLS-GFP) V 3 OH11062
otIs620(unc-11prom8::2xNLS-GFP) III 11 OH13606
otIs518(eat-4fosmid::SL2::mCherry::H2B, pha-1(+)) V; pha-1(e2123) III 32 OH13645
otIs653(srg-8prom::mCherry, cho-1prom::mCherry, srg-8prom::NLG-1::spGFP1-10, cho-1prom::NLG-1::spGFP11) This study OH15034
otIs748(rab-3prom1::GFP, ttx-3prom::mCherry) X This study OH16085
otDf1 X This study OH16102
ceh-44(ot1015[ceh-44::GFP]) III 12 OH16219
ceh-49(ot1016[ceh-49::GFP]) V 12 OH16224
otEx7463(ceh-48prom4:: 2xNLS-GFP, pha-1(+)); pha-1(e2123) III This study OH16284
otEx7481(mir-228prom::ceh-48::GFP); otIs356(rab-3prom1::2xNLS-tagRFP) V This study OH16356
ceh-44(ot1028) III This study OH16376
ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otIs356 V; otDf1 X This study OH16377
ceh-38(tm321) II; ceh-48(tm6112) IV; otIs356 V; otDf1 X This study OH16397
ceh-38(tm321) II; ceh-48(tm6112) IV This study OH16583
ceh-44(ot1028) III; ceh-48(tm6112) IV This study OH16584
ceh-38(tm321) II; otIs356 V This study OH16586
ceh-38(tm321) II; ceh-48(tm6112) IV; otIs356 V This study OH16587
ceh-48(tm6112) IV; otIs356 V This study OH16590
ceh-38(tm321) II;ceh-44(ot1028) III; ceh-48(tm6112) IV This study OH16593
nsIs198(mir-228prom::GFP); otIs356(rab-3prom1::2xNLS-tagRFP) V This study OH16602
otEx7617(unc-10prom12(ΔCUT)::2xNLS-GFP, pha-1(+)); pha-1(e2123) III This study OH16654
otEx7619(rab-3prom10(ΔCUT)::2xNLS-GFP, pha-1(+)); pha-1(e2123) III This study OH16656
otEx7644(ric-4prom30(ΔCUT)::2xNLS-GFP, pha-1(+)); pha-1(e2123) III This study OH16707
otEx7645(ric-4prom30:: 2xNLS-GFP, pha-1(+)); pha-1(e2123) III This study OH16708
otEx7646(unc-10prom12::2xNLS-GFP, pha-1(+)); pha-1(e2123) III This study OH16709
otIs788(cat-4prom::GFP::CLA-1, cat-4prom::mCherry, inx-16prom::tagRFP) This study OH16737
otIs790(UPN::npp-9::mCherry::blrp::3xflag) 27 OH16748
otIs794(cho-1fosmid::NLS-SL2-YFP-H2B, eat-4fosmid::SL2:: LSSmOrange-H2B, unc-47prom::tagBFP2, cat-1prom::mMaroon, rab3prom1::2xNLS-tagRFP) This study OH16765
ric-4(ot1123 syb2878) V This study OH17045
ceh-48(ot1125[ceh-48::GFP]) IV This study OH17051
ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otDf1 X; otIs790(UPN::npp-9::mCherry::blrp::3xflag) This study OH17055
rab-3(ot1178 syb3072) II This study OH17504
ric-4(ot1179 ot1123 syb2878) V This study OH17505
unc-10(ot1180 syb2898 syb3252) X This study OH17506
ric-4(ot1181 syb2878) V This study OH17507
ric-4(ot1182 syb2878) V This study OH17508
ric-4(ot1183 ot1181 syb2878) V This study OH17509
ceh-38(tm321) II; ceh-44(ot1028) III; unc-86(ot1184) III; ceh-48(tm6112) IV; otDf1 X This study OH17510
ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otDf1 X; ceh-14(ot1185) X This study OH17511
ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; unc-30(ot1186) IV; otDf1 X This study OH17512
unc-86(ot1184) III This study OH17513
ceh-14(ot1185) X This study OH17514
unc-30(ot1186) IV This study OH17515
otEx7814(rab-3prom10::2xNLS-GFP, pha-1(+)); pha-1(e2123) III This study OH17517
ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; ric-4(syb2878) V; otDf1 X This study OH17518
ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; egl-3(syb4478) V; otDf1 X This study OH17519
ceh-38(tm321) II; ceh-48(tm6112) IV; otDf1 X This study OH17520
ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otDf1 X This study OH17521
ceh-38(tm321) II; ceh-44(ot1028) III; otDf1 X; otIs653 This study OH17522
ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otDf1 X; otIs788 This study OH17523
ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otIs518 V; otDf1 X This study OH17524
ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otDf1 X; otIs794 This study OH17525
ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otDf1, otIs748 X This study OH17526
otEx7815(ceh-48prom4::ceh-48, ttx-3prom::GFP); ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otIs356 V; otDf1 X This study OH17527
otEx7816(ceh-48prom4::ceh-44, ttx-3prom::GFP); ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otIs356 V; otDf1 X This study OH17528
otEx7817(ceh-48prom4::ceh-38, ttx-3prom::GFP); ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otIs356 V; otDf1 X This study OH17529
otEx7818(ceh-48prom4::ceh-39, ttx-3prom::GFP); ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otIs356 V; otDf1 X This study OH17530
otEx7819(ceh-48prom4::hOC1, ttx-3prom::GFP); ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otIs356 V; otDf1 X This study OH17531
otEx7820(eft-3prom::ceh-48, ttx-3prom::GFP); ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otIs356 V; otDf1 X This study OH17532
otEx7821(eft-3prom::ceh-44, ttx-3prom::GFP); ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otIs356 V; otDf1 X This study OH17533
otEx7822(eft-3prom::ceh-38, ttx-3prom::GFP); ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otIs356 V; otDf1 X This study OH17534
otEx7823(eft-3prom::ceh-39, ttx-3prom::GFP); ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otIs356 V; otDf1 X This study OH17535
otEx7824(eft-3prom::hOC1, ttx-3prom::GFP); ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otIs356 V; otDf1 X This study OH17536
ceh-44(ot1028) III; otIs356 V This study OH17537
otIs356 V; otDf1 X This study OH17538
ceh-44(ot1028) III; ceh-48(tm6112) IV; otIs356 V This study OH17539
ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otIs356 V This study OH17540
otIs620 III; ceh-48(tm6112) IV This study OH17541
ceh-38(tm321) II; otIs620 III This study OH17542
otIs620 III; otDf1 X This study OH17543
ceh-38(tm321) II; otIs620 III; ceh-48(tm6112) IV This study OH17544
ceh-38(tm321) II; otIs620 III; ceh-48(tm6112) IV; otDf1 X This study OH17545
ceh-48(tm6112) IV; otIs381 V This study OH17546
ceh-44(ot1028) III; otIs381 V This study OH17547
ceh-38(tm321) II; otIs381 V This study OH17548
otIs381 V; otDf1 X This study OH17549
ceh-44(ot1028) III; ceh-48(tm6112) IV; otIs381 V This study OH17550
ceh-38(tm321) II; ceh-48(tm6112) IV; otIs381 V This study OH17551
ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otIs381 V This study OH17552
ceh-38(tm321) II; ceh-48(tm6112) IV; otIs381 V; otDf1 X This study OH17553
ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; otIs381 V; otDf1 X This study OH17554
ceh-38(tm321) II; ceh-44(ot1028) III; ceh-48(tm6112) IV; nova-1(syb4373) V; otDf1 X This study OH17584
wgIs241(ceh-38fosmid::TY1::EGFP::3xFLAG + unc-119(+)) 50 OP241
wgIs631(ceh-48fosmid::TY1::EGFP::3xFLAG + unc-119(+)) 50 OP631
wgIs759(ceh-41fosmid::TY1::EGFP::3xFLAG + unc-119(+)) 50 OP759
ric-4(syb2878[ric-4::T2A::3xNLS::GFP]) V This study PHX2878
rab-3(syb3072[rab-3::T2A::3xNLS::GFP]) II This study PHX3072
unc-10(syb2898 syb3252[unc-10::T2A::3xNLS::GFP]) X This study PHX3252
nova-1(syb4373[nova-1::GFP]) V This study PHX4373
rbm-25(syb4376[rbm-25::GFP]) V This study PHX4376
ehs-1(syb4426[ehs-1::SL2-GFP-H2B]) II This study PHX4426
egl-3(syb4478[egl-3::SL2-GFP-H2B]) V This study PHX4478
ehs-1(syb4426 syb4716) II This study PHX4716
ceh-38(syb4799[ceh-38::GFP]) II This study PHX4799
ceh-41(syb4901[ceh-41::GFP]) X This study PHX4901
tpan-1(syb5349[tpan-1::GFP]) V This study PHX5349
nova-1(syb4373 syb5446) V This study PHX5446
ric-4(md1088) V 18 RM956
Software and algorithms
ImageJ 56 https://imagej.nih.gov/ij/
Worm Tracker v2.0 47 https://www.mrc-lmb.cam.ac.uk/wormtracker/
Wormlab 46 MBF Bioscience
STAR 57 https://code.google.com/archive/p/rna-star/
featurecounts 58 http://subread.sourceforge.net/
DeSeq2 59 https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Gene Set Enrichment Analysis tool 60 https://wormbase.org/tools/enrichment/tea/tea.cgi
MEME-ChIP 45 https://meme-suite.org/meme/tools/meme-chip
Tomtom Motif Comparison Tool 61 https://meme-suite.org/meme/tools/tomtom
Other
Confocal Laser Scanning Microscope Zeiss LSM 880
Sequencing Platform Illumina NextSeq 500
Sorting Platform Union Biometrica COPAS FP-250
Disposable Tissue Grinder Fisher Scientific Cat# 02-542-09