{"database": "metadata", "table": "run_metadata", "rows": [[59316, "SRR11855602", "SRX8405703", "SRS6718144", "SRP264942", "PRJNA635369", "Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing", "GSE151273", "Transcriptome Analysis", "Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis  especially in neural tissues. Mutations in pre mRNAs processing factor 31 PRPF31 cause autosomal dominant retinitis pigmentosa  a progressive retinal degeneration disease. The transcriptome wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here  we showed that the differentiation and viability of retinal progenitor cells RPCs are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level  significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild type human PRPF31 rather than the disease associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak five prime splicing site. Moreover  genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events  which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis. Overall design: Head mRNA profiles of 36 hpf sibling wild type and prpf31 /  zebrafish were generated by deep sequence in three independent biological replicates.", null, "pubmed:33476374", null, "AB Head sib2", "GSM4570138", null, "source name:Head|strain:AB|tissue:Head|age:36 hpf type", "AB Head sib2", "Illumina Casava1.8 software used for basecalling. RNA seq reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 genome assembly using HISAT version 2.0.4. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM  of each gene was calculated based on the length of the gene and reads count mapped to this  gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per  Millions base pairs sequenced  considers the effect of sequencing depth and gene length  for the reads count at the same time  and is currently the most commonly used method for  estimating gene expression levels Trapnell  Cole  et al.  2010 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample Supplementary files format and content: tab delimited text files with raw gene counts for every gene and every sample", "Head", null, "Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer\u2019s recommendations and index codes were added to attribute sequences to each sample. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer\uff085X\uff09 . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase\uff08RNase H \uff09 . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3\u2019 ends of DNA fragments  NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length  the library fragments were purified with AMPure XP system Beckman Coulter  Beverly  USA. Then 3 \u00b5l USER Enzyme NEB  USA was used with size selected  adaptor ligated cDNA at 37\u00b0C for 15 min followed by 5 min at 95 \u00b0C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase  Universal PCR primers and Index X Primer. At last  PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system", null, "strain:AB|tissue:Head|age:36 hpf type", "GSM4570138", "GSM4570138: AB Head sib2; Danio rerio; RNA Seq", "GSM4570138", null, "1", "Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 \u00b5g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext\u00ae Ultra\u2122 RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer\uff085X\uff09 . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase\uff08RNase H \uff09 . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments  NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length  the library fragments were purified with AMPure XP system Beckman Coulter  Beverly  USA. Then 3 \u00b5l USER Enzyme NEB  USA was used with size selected  adaptor ligated cDNA at 37\u00b0C for 15 min followed by 5 min at 95 \u00b0C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase  Universal PCR primers and Index X Primer. At last  PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system", "GEO Accession:GSM4570138", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP264942", null, null, "sib2_1.fastq.gz sib2_2.fastq.gz", "fastq fastq", 12076874100.0, 40256247.0, "GSM4570138 r1", "0:150 1:150", "A:3116319895;C:2937698203;G:2949917740;T:3072719174;N:219088", 150, 150, null, null, 3116319895, 2937698203, 2949917740, 3072719174, 219088, "SRX8405703", "SRS6718144", "SRA1080304", "GEO", "Huazhong University of Science and Technology", 2, 0.95283, 0.95237, 0.06658, 0.06623, 0.69292, 0.69365, 0.44936, 0.45234, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "5prime", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "China", "2020-05-27", "Pharyngula", "Embryo", "Head", "Nervous System"]], "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": ["59316"], "units": {}, "query_ms": 10.895469997194596}