run_metadata: 34371

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	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.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	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	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
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