{"database": "metadata", "table": "run_metadata", "rows": [[63408, "SRR13785103", "SRX10170285", "SRS8320380", "SRP308232", "PRJNA704949", "miRNA overexpression modulates neutrophil migration", "GSE167554", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 31  miRNA 190 and miRNA 375  in neutrophils Overall design: For miRNA target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR 31  190  375 or vector control", null, null, null, "miR 375 2", "GSM5107441", null, "tissue:neutrophils|transgenic line:miR 375", "miR 375 2", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina NovaSeq 6000 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: \u201c s 0  p \u2013Q 10\u201d The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "neutrophils", "transgenic zebrafish lines were used to produce embryos. For miRNA target discovery  transgenic lines expressing miR 31  190  375 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grow to 3 dpf in embryonic media", "transgenic line:miR 375", "GSM5107441", "GSM5107441: miR 375 2; Danio rerio; RNA Seq", "GSM5107441", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM5107441", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP308232", null, null, "11_S27_R1_001.fastq.gz 11_S27_R2_001.fastq.gz", "fastq fastq", 6029914928.0, 29851064.0, "GSM5107441 r1", "0:101 1:101", "A:1615847350;C:1389005627;G:1392538803;T:1632327057;N:196091", 101, 101, null, null, 1615847350, 1389005627, 1392538803, 1632327057, 196091, "SRX10170285", "SRS8320380", "SRA1200205", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.70139, 0.70178, 0.12251, 0.1232, 0.84997, 0.84956, 0.64095, 0.63987, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-02-25", "Larval", "Larval", "Blood", "Hematopoietic 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": ["63408"], "units": {}, "query_ms": 6.939297003555112}