{"database": "metadata", "table": "run_metadata", "rows": [[38042, "SRR1371226", "SRX585640", "SRS631986", "SRP043064", "PRJNA252044", "Transcriptome Analysis Reveals a Comprehensive Regulatory Network Involved in the Zebrafish Model of Diamond Blackfan Anemia from RPL5 Deficiency [miRNA Seq]", "GSE58344", "Transcriptome Analysis", "In this study  we generated a zebrafish model of DBA with RPL5 morphants and implemented high throughput RNA seq and miRNA seq to identify key genes  lncRNAs  and miRNAs during zebrafish development and hematopoiesis. We found that RPL5 is required for both primitive and definitive hematopoiesis processes that are partially mediated by the P53 pathway. Several genes such as cirh1a  noc2l  tars  and nol6 and miRNAs such as dre miR 10a*  dre miR 722  dre miR 737  and dre miR 142a 3p were significantly deregulated  and these changes may play a crucial role in hematopoiesis  ribosome biogenesis and development process. We also characterized the lncRNome in zebrafish with RPL5 deficiency. By constructing a comprehensive regulatory network  we identified central node genes in the network connected to the P53 pathway  almost all of which were targeted by the significantly deregulated miRNAs listed above. Our results therefore establish a regulatory network for critical genes and miRNAs involved in the RPL5 deficient zebrafish model and provide a comprehensive basis for the molecular pathogenesis of RPL5 mediated DBA and other ribosomopathies. Overall design: Determine the differences of miRNome between RPL5 deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPL5 mediated human diseases", "parent bioproject:PRJNA252043", "pubmed:26961822", null, "RPL5 MO [miRNA]", "GSM1408095", null, "tissue:embryo|genotype/variation:RPL5 morpholino knockdown|developmental stage:48hpf", "RPL5 MO [miRNA]", "FASTX Toolkit clipper was used to remove sequencing adapters. The .fastq file was converted to a tab delimited file which held only the unique sequence read and its corresponding number of copies. The files were uploaded to DSAP http://dsap.cgu.edu.tw/index.htm for clustering of tags  classification of non coding small RNAs and miRNAs basis on sequencing homology search against the Rfam and miRBase database respectively. The differential expressed miRNAs were detected by R package DEGseq using the output data of DSAP. Genome build: Zv9", "embryo", "Zebrafish embryos at the one cell stage were injected with the MOs using an Microinjector WPI SYS PV830. Based on initial injection trials  2 5 ng MO and control MO was chosen as the optimal concentration.", "Immediately post harvesting  40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at  80\u00b0C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer\u2019s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer\u2019s instructions.", "Zebrafish embryos were kept in a 28.5\u2103 incubator to 48hpf", "genotype/variation:RPL5 morpholino knockdown|developmental stage:48hpf", "GSM1408095", "GSM1408095: RPL5 MO [miRNA]; Danio rerio; miRNA Seq", "GSM1408095", null, "1", "Immediately post harvesting  40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at  80\u00b0C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer\u2019s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer\u2019s instructions.", "GEO Accession:GSM1408095", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP043064", null, null, "s_7_IDX19_1.fq", "fastq", 1093234725.0, 13496725.0, "GSM1408095 r1", "0:81", "A:263908052;C:257987133;G:278889068;T:292410262;N:40210", 81, null, null, null, 263908052, 257987133, 278889068, 292410262, 40210, "SRX585640", "SRS631986", "SRA169796", "GEO", "Beijing Institute of Genomics", 1, 3e-05, null, 0.0, null, 0.99991, null, 0.5, null, 81, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2014-06-10", "Hatching", "Embryo", "Embryo Imprecise", "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": ["38042"], "units": {}, "query_ms": 12.43990699731512}