{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"size fractionation\", experiment.library_strategy = \"RNA-Seq\" and tissue_curation_coarse = \"Surface Structure\"", "rows": [[36272, "SRR298567", "SRX079845", "SRS212651", "SRP007331", "PRJNA141525", "Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.", "GSE29418", "Transcriptome Analysis", "RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.", null, "pubmed:21743441", null, "ZiliIPTes", "GSM727524", null, "tissue:RNA obtained from immunoprecipitation with Zili antibody|strain:TL", "ZiliIPTes", "three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.", "RNA obtained from immunoprecipitation with Zili antibody", null, "Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 \u00c2\u00b5l Dynabeads Invitrogen  3 or 6 testes  and Zili antibody in a total volume of 500 \u00c2\u00b5l.  RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis  adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.", null, "strain:TL", "GSM727524", "GSM727524: ZiliIPTes", "GSM727524: ZiliIPTes", "GSM727524: ZiliIPTes", "1", null, "GEO Accession:GSM727524", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP007331", null, "read name barcode proc directive:ignore", "ZiliIPTes.fastq", "fastq", 995759064.0, 27659974.0, "GSM727524 1", "0:36", null, 36, null, null, null, null, null, null, null, null, "SRX079845", "SRS212651", "SRA039167", "GEO", "European Research Institute for the Biology of Ageing, University Medical Center Groningen", 1, 0.0537, null, 0.03117, null, 0.95856, null, 0.42091, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2011-05-20", "Undetermined", "Undetermined", "Trunk", "Surface Structure"], [36335, "SRR398322", "SRX115580", "SRS285697", "SRP010291", "PRJNA150927", "miR 221 is required for endothelial tip cell behaviors during vascular development", "GSE35078", "Transcriptome Analysis", "Through deep sequencing and functional screening in zebrafish  we find that miR 221 is essential for angiogenesis. miR 221 knockdown phenocopied defects associated with loss of the tip cell expressed Flt4 receptor.  Furthermore  miR 221 was required for tip cell proliferation and migration  as well as tip cell potential in mosaic blood vessels.  miR 221 knockdown also prevented \u201chyper angiogenesis\u201d defects associated with Notch deficiency and miR 221 expression was inhibited by Notch signaling.  Finally  miR 221 promoted tip cell behavior through repression of two targets: cyclin dependent kinase inhibitor 1b cdkn1b and phosphoinositide 3 kinase regulatory subunit 1 pik3r1.  These results identify miR 221 as an important regulatory node through which tip cell migration and proliferation are controlled during angiogenesis. Overall design: Identification of endothelial expressed microRNA from FACS isolated zebrafish endothelial cells.", null, "pubmed:22340502", null, "miRNA GFP minus", "GSM861784", null, "source name:whole zebrafish embryos at 24 hpf|age:24 hpf|development stage:embryo|tissue:whole body|cell type:all cell types", "miRNA GFP minus", "The standard Illumina pipeline was applied for base calls and quality scoring; sequence tags were subsequently analyzed using miR Deep2.", "whole zebrafish embryos at 24 hpf", "Tgkdrl:egfp embryos were dissociated at 24 hpf  followed by fluorescence activated cell sorting to isolate GFP positive and  negative cells.", "Small RNAs were isolated by polyacrylamide gel electrophoresis and ligated to RNA adapters  followed by cDNA synthesis and amplification with Illumina primers.", null, "age:24 hpf|developmental stage:embryo|tissue:whole body|cell type:all cell types", "GSM861784", "GSM861784: miRNA GFP minus; Danio rerio; RNA Seq", "GSM861784 1", "GSM861784: 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vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized \"enhancer of microexon\" eMIC protein domain", null, null, "Pool of one hundred 8hpf embryos", "8hpf embryos", "Embr 8hpf", null, "strain:AB|dev stage:8hpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: 8hpf embryos", "Embr 8hpf", "Embr 8hpf", "RNA extracted from a pool of one hundred embryos", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP149913", null, null, "Embr_8hpf_R1-125.fq.gz Embr_8hpf_R2-125.fq.gz", "fastq fastq", 20486524750.0, 81946099.0, "Embr 8hpf R2 125.fq.gz", "0:125 1:125", "A:5437735333;C:4808439456;G:4859422420;T:5377132981;N:3794560", 125, 125, null, null, 5437735333, 4808439456, 4859422420, 5377132981, 3794560, "SRX4184227", "SRS3395607", "SRA717220", "Centre for 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body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: 12hpf embryos", "Embr 12hpf", "Embr 12hpf", "RNA extracted from a pool of one hundred embryos", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP149913", null, null, "Embr_12hpf_R2-125.fq.gz Embr_12hpf_R1-125.fq.gz", "fastq fastq", 22366284500.0, 89465138.0, "Embr 12hpf R1 125.fq.gz", "0:125 1:125", "A:5886492098;C:5284016845;G:5382041408;T:5809628253;N:4105896", 125, 125, null, null, 5886492098, 5284016845, 5382041408, 5809628253, 4105896, "SRX4184226", "SRS3395606", "SRA717220", "Centre for Genomic Regulation|Systems Biology Department", "Centre for Genomic Regulation", 2, 0.96226, 0.96763, 0.06393, 0.06451, 0.74355, 0.74472, 0.48233, 0.48387, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2019-01-22", "Segmentation", "Embryo", "Trunk", "Surface Structure"]], "truncated": false, "filtered_table_rows_count": 5, "expanded_columns": [], "expandable_columns": [], "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", 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