metadata: run_metadata: 23 rows where experiment.platform = "ELEMENT" and technology = "bulk"

23 rows where experiment.platform = "ELEMENT" and technology = "bulk"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
34364	34364	SRR31695142	SRX27056958	SRS23518718	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep4	GSM8678154	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:Knockdown Chemically Synthesized gRNA\|geo loc name:missing\|collection date:missing	RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep4	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:Knockdown Chemically Synthesized gRNA	GSM8678154	GSM8678154: RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep4; Danio rerio; RNA Seq	GSM8678154 r1	GSM8678154	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_g1Syn_rep4_R1.fastq.gz T_pRfxCas13d_g1Syn_rep4_R2.fastq.gz	fastq fastq	1869396000.0	12462640.0	GSM8678154 r1	0:75 1:75	A:497545631;C:434254877;G:436435676;T:501090064;N:69752	75	75	497545631	434254877	436435676	501090064	69752	SRX27056958	SRS23518718	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34365	34365	SRR31695143	SRX27056957	SRS23518717	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep3	GSM8678153	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:Knockdown Chemically Synthesized gRNA\|geo loc name:missing\|collection date:missing	RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep3	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:Knockdown Chemically Synthesized gRNA	GSM8678153	GSM8678153: RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep3; Danio rerio; RNA Seq	GSM8678153 r1	GSM8678153	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_g1Syn_rep3_R1.fastq.gz T_pRfxCas13d_g1Syn_rep3_R2.fastq.gz	fastq fastq	1939758450.0	12931723.0	GSM8678153 r1	0:75 1:75	A:510928336;C:455303431;G:458245636;T:515206838;N:74209	75	75	510928336	455303431	458245636	515206838	74209	SRX27056957	SRS23518717	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34366	34366	SRR31695144	SRX27056956	SRS23518716	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep4	GSM8678152	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:Knockdown Chemically Synthesized gRNA\|geo loc name:missing\|collection date:missing	RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep4	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:Knockdown Chemically Synthesized gRNA	GSM8678152	GSM8678152: RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep4; Danio rerio; RNA Seq	GSM8678152 r1	GSM8678152	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_g3Syn_rep4_R1.fastq.gz T_pRfxCas13d_g3Syn_rep4_R2.fastq.gz	fastq fastq	1372458150.0	9149721.0	GSM8678152 r1	0:75 1:75	A:363668106;C:319963774;G:322725620;T:366049498;N:51152	75	75	363668106	319963774	322725620	366049498	51152	SRX27056956	SRS23518716	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34367	34367	SRR31695145	SRX27056955	SRS23518715	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep3	GSM8678151	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:Knockdown Chemically Synthesized gRNA\|geo loc name:missing\|collection date:missing	RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep3	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:Knockdown Chemically Synthesized gRNA	GSM8678151	GSM8678151: RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep3; Danio rerio; RNA Seq	GSM8678151 r1	GSM8678151	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_g3Syn_rep3_R1.fastq.gz T_pRfxCas13d_g3Syn_rep3_R2.fastq.gz	fastq fastq	1716718500.0	11444790.0	GSM8678151 r1	0:75 1:75	A:454308432;C:401470287;G:402968652;T:457908108;N:63021	75	75	454308432	401470287	402968652	457908108	63021	SRX27056955	SRS23518715	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34368	34368	SRR31695150	SRX27056954	SRS23518714	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d control rep6	GSM8678150	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:RfxCas13d control\|geo loc name:missing\|collection date:missing	RfxCas13d control rep6	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:RfxCas13d control	GSM8678150	GSM8678150: RfxCas13d control rep6; Danio rerio; RNA Seq	GSM8678150 r1	GSM8678150	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_rep6_R1.fastq.gz T_pRfxCas13d_rep6_R2.fastq.gz	fastq fastq	1820554200.0	12137028.0	GSM8678150 r1	0:75 1:75	A:480817156;C:426951021;G:428763810;T:483952927;N:69286	75	75	480817156	426951021	428763810	483952927	69286	SRX27056954	SRS23518714	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34369	34369	SRR31695146	SRX27056953	SRS23518713	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep2	GSM8678149	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:Knockdown Chemically Synthesized gRNA\|geo loc name:missing\|collection date:missing	RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep2	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:Knockdown Chemically Synthesized gRNA	GSM8678149	GSM8678149: RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep2; Danio rerio; RNA Seq	GSM8678149 r1	GSM8678149	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_g1Syn_rep2_R1.fastq.gz T_pRfxCas13d_g1Syn_rep2_R2.fastq.gz	fastq fastq	1686506550.0	11243377.0	GSM8678149 r1	0:75 1:75	A:445306390;C:395515087;G:396951869;T:448671449;N:61755	75	75	445306390	395515087	396951869	448671449	61755	SRX27056953	SRS23518713	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34370	34370	SRR31695147	SRX27056952	SRS23518712	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep1	GSM8678148	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:Knockdown Chemically Synthesized gRNA\|geo loc name:missing\|collection date:missing	RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep1	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:Knockdown Chemically Synthesized gRNA	GSM8678148	GSM8678148: RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep1; Danio rerio; RNA Seq	GSM8678148 r1	GSM8678148	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_g1Syn_rep1_R1.fastq.gz T_pRfxCas13d_g1Syn_rep1_R2.fastq.gz	fastq fastq	2099239050.0	13994927.0	GSM8678148 r1	0:75 1:75	A:555464950;C:490168575;G:492715156;T:560811934;N:78435	75	75	555464950	490168575	492715156	560811934	78435	SRX27056952	SRS23518712	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34371	34371	SRR31695148	SRX27056951	SRS23518711	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep2	GSM8678147	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:Knockdown Chemically Synthesized gRNA\|geo loc name:missing\|collection date:missing	RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep2	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:Knockdown Chemically Synthesized gRNA	GSM8678147	GSM8678147: RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep2; Danio rerio; RNA Seq	GSM8678147 r1	GSM8678147	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_g3Syn_rep2_R1.fastq.gz T_pRfxCas13d_g3Syn_rep2_R2.fastq.gz	fastq fastq	1855616550.0	12370777.0	GSM8678147 r1	0:75 1:75	A:490735862;C:434070234;G:436325424;T:494415408;N:69622	75	75	490735862	434070234	436325424	494415408	69622	SRX27056951	SRS23518711	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34372	34372	SRR31695149	SRX27056950	SRS23518710	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep1	GSM8678146	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:Knockdown Chemically Synthesized gRNA\|geo loc name:missing\|collection date:missing	RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep1	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:Knockdown Chemically Synthesized gRNA	GSM8678146	GSM8678146: RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep1; Danio rerio; RNA Seq	GSM8678146 r1	GSM8678146	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_g3Syn_rep1_R1.fastq.gz T_pRfxCas13d_g3Syn_rep1_R2.fastq.gz	fastq fastq	2029890750.0	13532605.0	GSM8678146 r1	0:75 1:75	A:536398630;C:474872197;G:478734292;T:539809587;N:76044	75	75	536398630	474872197	478734292	539809587	76044	SRX27056950	SRS23518710	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34373	34373	SRR31695155	SRX27056949	SRS23518709	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d control rep5	GSM8678145	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:RfxCas13d control\|geo loc name:missing\|collection date:missing	RfxCas13d control rep5	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:RfxCas13d control	GSM8678145	GSM8678145: RfxCas13d control rep5; Danio rerio; RNA Seq	GSM8678145 r1	GSM8678145	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_rep5_R1.fastq.gz T_pRfxCas13d_rep5_R2.fastq.gz	fastq fastq	1699800000.0	11332000.0	GSM8678145 r1	0:75 1:75	A:448834438;C:398037498;G:400242751;T:452619971;N:65342	75	75	448834438	398037498	400242751	452619971	65342	SRX27056949	SRS23518709	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34374	34374	SRR31695151	SRX27056948	SRS23518708	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d + g3 IVTed si:dkey 93m18.4 rep3	GSM8678144	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:Knockdown IVTed gRNA\|geo loc name:missing\|collection date:missing	RfxCas13d + g3 IVTed si:dkey 93m18.4 rep3	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:Knockdown IVTed gRNA	GSM8678144	GSM8678144: RfxCas13d + g3 IVTed si:dkey 93m18.4 rep3; Danio rerio; RNA Seq	GSM8678144 r1	GSM8678144	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_g3_rep3_R1.fastq.gz T_pRfxCas13d_g3_rep3_R2.fastq.gz	fastq fastq	1603289100.0	10688594.0	GSM8678144 r1	0:75 1:75	A:420349766;C:379529179;G:379756700;T:423592677;N:60778	75	75	420349766	379529179	379756700	423592677	60778	SRX27056948	SRS23518708	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34375	34375	SRR31695154	SRX27056947	SRS23518706	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d + g3 IVTed si:dkey 93m18.4 rep2	GSM8678143	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:Knockdown IVTed gRNA\|geo loc name:missing\|collection date:missing	RfxCas13d + g3 IVTed si:dkey 93m18.4 rep2	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:Knockdown IVTed gRNA	GSM8678143	GSM8678143: RfxCas13d + g3 IVTed si:dkey 93m18.4 rep2; Danio rerio; RNA Seq	GSM8678143 r1	GSM8678143	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_g3_rep2_R1.fastq.gz T_pRfxCas13d_g3_rep2_R2.fastq.gz	fastq fastq	1700840400.0	11338936.0	GSM8678143 r1	0:75 1:75	A:447219410;C:401375108;G:401866426;T:450317233;N:62223	75	75	447219410	401375108	401866426	450317233	62223	SRX27056947	SRS23518706	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34376	34376	SRR31695152	SRX27056946	SRS23518707	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d control rep4	GSM8678142	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:RfxCas13d control\|geo loc name:missing\|collection date:missing	RfxCas13d control rep4	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:RfxCas13d control	GSM8678142	GSM8678142: RfxCas13d control rep4; Danio rerio; RNA Seq	GSM8678142 r1	GSM8678142	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_rep4_R1.fastq.gz T_pRfxCas13d_rep4_R2.fastq.gz	fastq fastq	1390819050.0	9272127.0	GSM8678142 r1	0:75 1:75	A:365774543;C:327280225;G:328329658;T:369385513;N:49111	75	75	365774543	327280225	328329658	369385513	49111	SRX27056946	SRS23518707	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34377	34377	SRR31695153	SRX27056945	SRS23518705	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d + g3 IVTed si:dkey 93m18.4 rep1	GSM8678141	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:Knockdown IVTed gRNA\|geo loc name:missing\|collection date:missing	RfxCas13d + g3 IVTed si:dkey 93m18.4 rep1	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:Knockdown IVTed gRNA	GSM8678141	GSM8678141: RfxCas13d + g3 IVTed si:dkey 93m18.4 rep1; Danio rerio; RNA Seq	GSM8678141 r1	GSM8678141	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_g3_rep1_R1.fastq.gz T_pRfxCas13d_g3_rep1_R2.fastq.gz	fastq fastq	1979083650.0	13193891.0	GSM8678141 r1	0:75 1:75	A:521444446;C:467332323;G:468450230;T:521779923;N:76728	75	75	521444446	467332323	468450230	521779923	76728	SRX27056945	SRS23518705	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34378	34378	SRR31695156	SRX27056944	SRS23518704	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d control rep3	GSM8678140	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:RfxCas13d control\|geo loc name:missing\|collection date:missing	RfxCas13d control rep3	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:RfxCas13d control	GSM8678140	GSM8678140: RfxCas13d control rep3; Danio rerio; RNA Seq	GSM8678140 r1	GSM8678140	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_rep3_R1.fastq.gz T_pRfxCas13d_rep3_R2.fastq.gz	fastq fastq	1520356800.0	10135712.0	GSM8678140 r1	0:75 1:75	A:400447283;C:357034714;G:358393387;T:404426537;N:54879	75	75	400447283	357034714	358393387	404426537	54879	SRX27056944	SRS23518704	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34379	34379	SRR31695157	SRX27056943	SRS23518703	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d + g1 IVTed si:dkey 93m18.4 rep3	GSM8678139	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:Knockdown IVTed gRNA\|geo loc name:missing\|collection date:missing	RfxCas13d + g1 IVTed si:dkey 93m18.4 rep3	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:Knockdown IVTed gRNA	GSM8678139	GSM8678139: RfxCas13d + g1 IVTed si:dkey 93m18.4 rep3; Danio rerio; RNA Seq	GSM8678139 r1	GSM8678139	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_g1_rep3_R1.fastq.gz T_pRfxCas13d_g1_rep3_R2.fastq.gz	fastq fastq	1890203250.0	12601355.0	GSM8678139 r1	0:75 1:75	A:501821472;C:441868721;G:441485425;T:504956362;N:71270	75	75	501821472	441868721	441485425	504956362	71270	SRX27056943	SRS23518703	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34380	34380	SRR31695162	SRX27056942	SRS23518702	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d + g2 IVTed si:dkey 93m18.4 rep3	GSM8678138	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:Knockdown IVTed gRNA\|geo loc name:missing\|collection date:missing	RfxCas13d + g2 IVTed si:dkey 93m18.4 rep3	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:Knockdown IVTed gRNA	GSM8678138	GSM8678138: RfxCas13d + g2 IVTed si:dkey 93m18.4 rep3; Danio rerio; RNA Seq	GSM8678138 r1	GSM8678138	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_g2_rep3_R1.fastq.gz T_pRfxCas13d_g2_rep3_R2.fastq.gz	fastq fastq	1839509400.0	12263396.0	GSM8678138 r1	0:75 1:75	A:485779725;C:432231942;G:432933832;T:488492257;N:71644	75	75	485779725	432231942	432933832	488492257	71644	SRX27056942	SRS23518702	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34381	34381	SRR31695158	SRX27056941	SRS23518701	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d + g1 IVTed si:dkey 93m18.4 rep2	GSM8678137	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:Knockdown IVTed gRNA\|geo loc name:missing\|collection date:missing	RfxCas13d + g1 IVTed si:dkey 93m18.4 rep2	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:Knockdown IVTed gRNA	GSM8678137	GSM8678137: RfxCas13d + g1 IVTed si:dkey 93m18.4 rep2; Danio rerio; RNA Seq	GSM8678137 r1	GSM8678137	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_g1_rep2_R1.fastq.gz T_pRfxCas13d_g1_rep2_R2.fastq.gz	fastq fastq	1742339250.0	11615595.0	GSM8678137 r1	0:75 1:75	A:461346904;C:406656276;G:409937021;T:464333259;N:65790	75	75	461346904	406656276	409937021	464333259	65790	SRX27056941	SRS23518701	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34382	34382	SRR31695161	SRX27056940	SRS23518700	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d control rep2	GSM8678136	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:RfxCas13d control\|geo loc name:missing\|collection date:missing	RfxCas13d control rep2	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:RfxCas13d control	GSM8678136	GSM8678136: RfxCas13d control rep2; Danio rerio; RNA Seq	GSM8678136 r1	GSM8678136	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_rep2_R1.fastq.gz T_pRfxCas13d_rep2_R2.fastq.gz	fastq fastq	1800739800.0	12004932.0	GSM8678136 r1	0:75 1:75	A:477337887;C:421087001;G:421493244;T:480753457;N:68211	75	75	477337887	421087001	421493244	480753457	68211	SRX27056940	SRS23518700	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34383	34383	SRR31695159	SRX27056939	SRS23518699	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d + g2 IVTed si:dkey 93m18.4 rep2	GSM8678135	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:Knockdown IVTed gRNA\|geo loc name:missing\|collection date:missing	RfxCas13d + g2 IVTed si:dkey 93m18.4 rep2	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:Knockdown IVTed gRNA	GSM8678135	GSM8678135: RfxCas13d + g2 IVTed si:dkey 93m18.4 rep2; Danio rerio; RNA Seq	GSM8678135 r1	GSM8678135	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_g2_rep2_R1.fastq.gz T_pRfxCas13d_g2_rep2_R2.fastq.gz	fastq fastq	1752030300.0	11680202.0	GSM8678135 r1	0:75 1:75	A:462116558;C:411708555;G:412346341;T:465792629;N:66217	75	75	462116558	411708555	412346341	465792629	66217	SRX27056939	SRS23518699	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34384	34384	SRR31695160	SRX27056938	SRS23518698	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d + g1 IVTed si:dkey 93m18.4 rep1	GSM8678134	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:Knockdown IVTed gRNA\|geo loc name:missing\|collection date:missing	RfxCas13d + g1 IVTed si:dkey 93m18.4 rep1	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:Knockdown IVTed gRNA	GSM8678134	GSM8678134: RfxCas13d + g1 IVTed si:dkey 93m18.4 rep1; Danio rerio; RNA Seq	GSM8678134 r1	GSM8678134	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_g1_rep1_R1.fastq.gz T_pRfxCas13d_g1_rep1_R2.fastq.gz	fastq fastq	1724105250.0	11494035.0	GSM8678134 r1	0:75 1:75	A:456793309;C:403294318;G:403256373;T:460696014;N:65236	75	75	456793309	403294318	403256373	460696014	65236	SRX27056938	SRS23518698	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34385	34385	SRR31695163	SRX27056937	SRS23518697	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d + g2 IVTed si:dkey 93m18.4 rep1	GSM8678133	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:Knockdown IVTed gRNA\|geo loc name:missing\|collection date:missing	RfxCas13d + g2 IVTed si:dkey 93m18.4 rep1	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:Knockdown IVTed gRNA	GSM8678133	GSM8678133: RfxCas13d + g2 IVTed si:dkey 93m18.4 rep1; Danio rerio; RNA Seq	GSM8678133 r1	GSM8678133	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_g2_rep1_R1.fastq.gz T_pRfxCas13d_g2_rep1_R2.fastq.gz	fastq fastq	1903402350.0	12689349.0	GSM8678133 r1	0:75 1:75	A:501904806;C:447043548;G:448270395;T:506113883;N:69718	75	75	501904806	447043548	448270395	506113883	69718	SRX27056937	SRS23518697	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures
34386	34386	SRR31695164	SRX27056936	SRS23518696	SRP551059	PRJNA1197382	Enhanced RNA targeting CRISPR Cas technology in zebrafish V	GSE284120	Transcriptome Analysis	Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized	parent bioproject:PRJNA1128082	pubmed:40091120	RfxCas13d control rep1	GSM8678132	source name:whole embryo\|tissue:whole embryo\|age:4 hpf\|treatment:RfxCas13d control\|geo loc name:missing\|collection date:missing	RfxCas13d control rep1	Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample	whole embryo	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer’s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	tissue:whole embryo\|age:4 hpf\|treatment:RfxCas13d control	GSM8678132	GSM8678132: RfxCas13d control rep1; Danio rerio; RNA Seq	GSM8678132 r1	GSM8678132	1	Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 µL of IDT indexed primers using xGen™ Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 µL of library and 5 µL of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55°C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 µL of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ELEMENT	Element AVITI	SRP551059	T_pRfxCas13d_rep1_R1.fastq.gz T_pRfxCas13d_rep1_R2.fastq.gz	fastq fastq	1980525450.0	13203503.0	GSM8678132 r1	0:75 1:75	A:522445746;C:464027491;G:467474918;T:526505284;N:72011	75	75	522445746	464027491	467474918	526505284	72011	SRX27056936	SRS23518696	SRA2032641	Stowers Institute for Medical Research	Stowers Institute for Medical Research	B	B	biological fallback assumption	element	element	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2024-12-12	Blastula	Embryo	Whole Organism	All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;