{"database": "metadata", "table": "run_metadata", "rows": [[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", null, "RfxCas13d + g3 IVTed si:dkey 93m18.4  rep1", "GSM8678141", null, "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", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050  Zymo Research following manufacturer\u2019s 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 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C 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 \u00b5L 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.", null, "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 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers  96 reactions  Cat No. 10005921 was added to 3 \u00b5L of library  and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C 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 \u00b5L 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "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, null, null, 521444446, 467332323, 468450230, 521779923, 76728, "SRX27056945", "SRS23518705", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["34377"], "units": {}, "query_ms": 7.525086999521591}