REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains
E. coli DH5α	New England Biolabs	C2987I
E. coli Rosetta™(DE3)	NOVAGEN Healthcare	70954-3
Chemicals, peptides, and recombinant proteins
LB broth (LB Lennox)	Condalab	1231
Bacteriological american agar	Condalab	1802
Chloramphenicol	Sigma-Aldrich	C0378-5G
Kanamycin A sulfate	Sigma-Aldrich	K4000-5G
IPTG	Protein Ark	GEN-S-02122-25G
Precision Plus Protein Standard All Blue	Bio-Rad Laboratories	161-0373
UltraPure Tris	Invitrogen	15504-020
HCl	Scharlau	AC0741
Polyethylene glycol 8000 (PEG)	Sigma-Aldrich	P2139
Dimethyl sulfoxide (DMSO)	PanReac	361954
MgSO4·7H2O	Sigma-Aldrich	M7774
2-[4-(2-hydroxyethyl) piperazin-1-yl] ethanesulfonic acid (HEPES)	Fisher Scientific	BP310-500
KOH	Merck	105032
KCl	Sigma-Aldrich	P3911-500G
DTT	Thermo Scientific	R0862
Glycerol	Fisher Scientific	BP229-4
Imidazole	Sigma-Aldrich	56748-250G
TURBO-DNase	Ambion	AM2238
Sodium Acetate	Sigma-Aldrich	23424-28-4
NaCl	Sigma-Aldrich	7647-14-5
KCl	Sigma-Aldrich	7447-40-7
NaHCO3	Sigma-Aldrich	144-55-8
Tween20	Sigma-Aldrich	P1379
SDS	GE Healthcare	17-1313-01
Bromophenol Blue	GE Healthcare	17-1329-01
10% TGX Stain-FreeTM FastCastTM Acrylamide Solutions	Bio-Rad Laboratories	1610183
Methylene blue	Sigma-Aldrich	122965-43-9
Tris Low EDTA	Sigma-Aldrich	T2194-100ML
Ethidium bromide	Sigma-Aldrich	1239-45-8
Restriction Enzymes	New England Biolabs	NEB
Q5® High-Fidelity DNA Polymerase	New England Biolabs	M0491
Gel Loading Dye, Purple (6×)	New England Biolabs	B7025
Gel Loading Buffer II (6×)	Thermo Fisher Scientific	8546G
InstantBlue Coomassie Protein Stain	Abcam	ISB1L
Agarose D1 Low EEO	Condalab	8010
Critical commercial assays
AmpliScribe-T7-Flash transcription	Epicenter	ASF3507
Qubit™ RNA BR Assay Kit	Thermo Fisher Scientific	Q10210
mMachine T3	Ambion	AM1348
mMachine SP6	Ambion	AM1340
RNeasy Mini Kit (Qiagen)	Qiagen	74104
RC-DC™ Protein Assay Kit	Bio-Rad Laboratories	5000122
30K Amicon Ultra-15	Merck Millipore	UFC9030
Favorprep Gel/PCR purification kit	Favorgen	FAGCK 001
PureLink PCR Purification Kit	Thermo Fisher Scientific(invitrogen)	K310001
Other
Incubator shaker	New Brunswick	Innova 42
Horizontal laminar flow cabinet	Cruma	HZ-2
Spectrophotometer	Shimadzu	UV-1280
Centrifuge (for microtubes)	Eppendorf	5415-R
Centrifuge (for Falcon tubes)	Eppendorf	5804-R
Centrifuge (for big volumes)	Thermo Scientific	Sorvall Lynx 6000
Thermoblock	Labnet International	Accublock D1100
pH-meter	Hach	SensION+ PH3
pH probe	Hach	5014
Sonicator	Branson	SFX 550
3/4" High-Gain Horn	Branson	101-147-035R
250 mL Rosette Glass Cooling Cell	Branson	201-123-003
ÄKTA Pure 25 L1 (Liquid Chromatography automated system)	GE Healthcare	29-0148-31
Absorbance detector U9-M (Liquid Chromatography automated system)	GE Healthcare	28-9340-89
Fraction collector F9-R (Liquid Chromatography automated system)	GE Healthcare	29-0113-62
His-Trap FF 1 mL column	GE Healthcare	17-5319-01
HiPrep 16/60 Sephacryl S-200 HR column	GE Healthcare	17-1166-01
SuperLoop 10 mL	GE Healthcare	18-1113-81
Amicon Ultra-15 (Centrifugal Filter Units)	Merck Millipore	UFC903024
Qubit® 3.0 Fluorometer	Life technology	Q33216
NanodropTM 2000	Thermo Scientific	ND-2000
Microinjector	Narishige	IM-300
Stereomicroscope	Leica Microsystems	KL300-LED
Forceps Dumont #55	Cibertec	11255-20
Acrodisc syringe filters 0.45 μm	Pall corporation	4654
50 mL Erlenmeyer flasks	Eulabor	EFN3-050-012
2 L Erlenmeyer flasks	Eulabor	EFN3-2K0-001
Petri dishes	Fisher Scientific	12644785
50 mL centrifuge tubes	VWR	525-1113
500 mL centrifuge tubes	Thermo Scientific	3141-0500
Clark Capillary Glass (1.0 OD × 0.58 ID × 100 L mm)	Panlab (Harvard Apparatus)	W3-30-0019
Experimental models: Organisms/strains
Zebrafish	Stowers/CABD	Strains AB/Tübingen (AB/Tu), AB, TF and TLF
Recombinant DNA
pT3TS-RfxCas13d	Kushawah et al. (2020)	Addgene plasmid #141320
pT3TS-RfxCas13d-NLS	Kushawah et al. (2020)	Addgene plasmid #141321
pET28B-RfxCas13d-His	Kushawah et al. (2020)	Addgene plasmid #141322
Oligonucleotides
Universal primer	Kushawah et al. (2020)	5′TAATACGACTCACTATAGGAACCCCTACC AACTGGTCGGGGTTTGAAAC
Universal primer with Stem loop disruption	Wessels et al. (2020)	5′TAATACGACTCACTATAGGTACCCCTACC AACTGGTCGGGGTTTGAAAC
tbxta_4	Kushawah et al. (2020)	5′AGCACCCGTATCTTTCAGCAAAGTTTCAA ACCCCGACCAGTT
tbxta_5	Kushawah et al. (2020)	5′GTGAGAGATACTCCAGCTTGAGGTTTCAA ACCCCGACCAGTT
tbxta_6	Kushawah et al. (2020)	5′TCGGTCCTGCTGGATTTTGTGGGTTTCAA ACCCCGACCAGTT
Tbxta_Fw	Kushawah et al. (2020)	5′CGCAAGACTTCCGGAAGAGT
Tbxta_Rv	Kushawah et al. (2020)	5′GAACCACAGAGCTGCTCCAT
Software and algorithms
RNAfold software	RNAfold web server	http://rna.tbi.univie.ac.at//cgi-bin/RNAWebSuite/RNAfold.cgi
Unicorn (for chromatography system)	GE Healthcare	7.1.0.378
Image Lab Standard Edition (for SDS-PAGE analysis)	Bio-Rad Laboratories	6.0.1.34
Mammalian cell culture-based algorithm to predict CRISPR-RfxCas13d activity	Sanjana Lab (NYU, NY, USA)	https://cas13design.nygenome.org/
Deposited data
Original data	This paper	Stowers Original Data Repository https://www.stowers.org/research/publications/libpb-1653