run_metadata: 32935
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 |
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| 32935 | SRR29524807 | SRX25034958 | SRS21734129 | SRP515684 | PRJNA1127455 | Enhanced RNA targeting CRISPR Cas technology in zebrafish I | GSE270527 | 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 efficacy of ex vivo computational models predicting in vivo mRNA depletion using data from 200 gRNAs in 8 cocktails of 25 gRNAs 10 pg/embryo | parent bioproject:PRJNA1128082 | pubmed:40091120 | RfxCas13d control rep2 | GSM8346200 | source name:whole embryo|tissue:whole embryo|cell line:4 hpf|cell type: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. Libraries were generated with the Mosquito HV Genomics SPT Labtech nanoliter liquid handling instrument using the Nextera XT DNA Library Preparation Kit Illumina FC 131 1096 at 1/8th reaction volumes paired with IDT for Illumina DNA/RNA UD Indexes Set A Illumina 20027213 and purified using the Ampure XP bead based reagent Beckman Coulter Cat. No. A63882. | tissue:whole embryo|cell line:4 hpf|cell type:RfxCas13d control | GSM8346200 | GSM8346200: RfxCas13d control rep2; Danio rerio; RNA Seq | GSM8346200 r1 | GSM8346200 | 1 | Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Libraries were generated with the Mosquito HV Genomics SPT Labtech nanoliter liquid handling instrument using the Nextera XT DNA Library Preparation Kit Illumina FC 131 1096 at 1/8th reaction volumes paired with IDT for Illumina DNA/RNA UD Indexes Set A Illumina 20027213 and purified using the Ampure XP bead based reagent Beckman Coulter Cat. No. A63882. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP515684 | RfxCas13d_R2_a.fastq.gz | fastq | 84322630.0 | 1204609.0 | GSM8346200 r1 | 0:70 | A:22796111;C:19390347;G:19371692;T:22760579;N:3901 | 70 | 22796111 | 19390347 | 19371692 | 22760579 | 3901 | SRX25034958 | SRS21734129 | SRA1907176 | Stowers Institute for Medical Research | Stowers Institute for Medical Research | 1 | 0.95152 | 0.12414 | 0.74608 | 0.52074 | 70 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | nextera | bulk | unknown | unknown | United States | 2024-06-24 | Blastula | Embryo | Whole Organism | All anatomical structures |