{"database": "metadata", "table": "run_metadata", "rows": [[37906, "SRR1138229", "SRX445322", "SRS540473", "SRP035565", "PRJNA236050", "Systematic Transcriptome Analysis of Zebrafish Model of Diamond Blackfan Anemia from RPS24 Deficiency miRNA Seq", "GSE54259", "Transcriptome Analysis", "In this study  we found RPS24 is required for both the primitive hematopoiesis and definitive hematopoiesis process partly mediated by P53 pathway. With the RNA seq and miRNA seq technique  several deregulated genes and miRNAs were found to be related with hematopoiesis  vascular development and apoptosis process in RPS24 deficient zebrafish. Meanwhile  a comprehensive regulatory network was firstly constructed to indentify the mechanisms of key miRNAs and gene pathways in this Model of Diamond Blackfan Anemia. Interestingly  we found that the central nodes genes in the network were almost all targeted by significantly deregulated miRNAs  with partial verification from previous studies  revealing that our network based approach is promising for the identification of new and important miRNAs in DBA. The present study provided comprehensive potential pathogenic genes and miRNAs data that are associated with RPS24 deficient zebrafish embryos as a model of DBA  which should provide a valuable resource for understanding the complex molecular pathogenesis of mutant RPS24 mediated human diseases. Overall design: Determine the differences of miRNome between RPS24 deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPS24 mediated human diseases", "parent bioproject:PRJNA236073", "pubmed:25189322;pubmed:26961822", null, "morpholino control miRNA Seq", "GSM1311218", null, "tissue:embryo|genotype:control morpholino|developmental stage:embryo 48hpf", "morpholino control miRNA Seq", "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:control morpholino|developmental stage:embryo 48hpf", "GSM1311218", "GSM1311218: morpholino control miRNA Seq; Danio rerio; RNA Seq", "GSM1311218", 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:GSM1311218", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP035565", null, null, "s_8_IDX21_1.fq", "fastq", 308681847.0, 3810887.0, "GSM1311218 r1", "0:81", "A:63686404;C:75263287;G:80056961;T:89650625;N:24570", 81, null, null, null, 63686404, 75263287, 80056961, 89650625, 24570, "SRX445322", "SRS540473", "SRA128456", "GEO", "Beijing Institute of Genomics", 1, 8e-05, null, 2e-05, null, 0.99991, null, 0.42857, null, 81, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2014-01-21", "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": ["37906"], "units": {}, "query_ms": 13.744233001489192}