{"database": "metadata", "table": "run_metadata", "rows": [[53427, "SRR9854014", "SRX6608456", "SRS5172704", "SRP216689", "PRJNA557179", "Role of the Exon Junction Complex in Danio rerio", "GSE135019", "Transcriptome Analysis", "The exon  junction complex EJC is composed of three core proteins Rbm8a  Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq.  We find that  as in human cells  zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant  magoh mutant and wild type sibling embryos.  This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants", null, null, null, "RBM8A RIPSEQ Rep3", "GSM3983830", null, "tissue:Whole embryo|developmental stage:24 hpf|rip antibody:Human Y14 Sigma  cat# Y1253|genotype/variation:RBM8A", "RBM8A RIPSEQ Rep3", "Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters  m 20   discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters  p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters  s  c  F 0.51  sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples", "Whole embryo", "None NA", "RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al.  Methods Mol Biol. 2018;1680:1 28. Briefly  a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product  which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.", "All embryos were raised at 28.5C upto the required developmental timepoint.", "developmental stage:24 hpf|rip antibody:Human Y14 Sigma  cat# Y1253|genotype/variation:RBM8A", "GSM3983830", "GSM3983830: RBM8A RIPSEQ Rep3; Danio rerio; RIP Seq", "GSM3983830", null, "1", "RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al.  Methods Mol Biol. 2018;1680:1 28. Briefly  a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product  which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.", "GEO Accession:GSM3983830", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP216689", null, "loader:fastq load.py", "ripseqB3.fastq.gz", "fastq", 1174462616.0, 32753220.0, "GSM3983830 r1", "0:35.86", "A:277856243;C:303697175;G:340240303;T:252574884;N:94011", 35, null, null, null, 277856243, 303697175, 340240303, 252574884, 94011, "SRX6608456", "SRS5172704", "SRA928193", "GEO", "Guramrit Singh, Molecular Genetics, The Ohio State University", 1, 0.90426, null, 0.1746, null, 0.77341, null, 0.57553, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-07-29", "Pharyngula", "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": ["53427"], "units": {}, "query_ms": 10.456119998707436}