{"database": "metadata", "table": "run_metadata", "rows": [[55353, "SRR10312405", "SRX7023625", "SRS5544401", "SRP226227", "PRJNA578399", "RNA seq of etv2 mutant knock in heterozygous and homozygous zebrafish embryos", "GSE139108", "Transcriptome Analysis", "Zebrafish etv2^Gt2A Gal4ci32 line was generated using CRISPR Cas9 mediated NHEJ approach which has 2A Gal4 sequence inserted with the exon 5 of etv2 gene thus interrupting etv2 coding sequence. Heterozygous and homozogous embryos were subjected to bulk RNA seq Overall design: 3 batches of 15 20 heterozygous and homozygous embryos were frozen at the 15 somite and 24 hpf stages. Total 12 samples were sequenced: triplicate samples of Heterozygous and homozygous embryos at 15 somite and 24 hpf stages", null, "pubmed:31705559", null, "etv2 homo 15som 1", "GSM4131105", null, "source name:Whole embryos|tissue:Whole embryos|line allele:etv2^Gt2A Gal4ci32|genotype:Homozygous|embryo stage:15 somite", "etv2 homo 15som 1", "Sequencing was performed at 20M PE 150 read depth by Novogene Inc Alignment to the zebrafish genome was performed using Strand 3.0 software using default parameters. Genome build: Zv9 Supplementary files format and content: Excel files include triplicate samples from heterozygous or homozygous embryos at each stage. DESeq normalized log scaled RPKM values are provided", "Whole embryos", "3 batches of heterozygous and homozygous embryos 15 20 embryos each were sorted based on GFP expression pattern and frozen on dry ice.", "Bulk RNA was purified using RNA quous 4 PCR kit ThermoFisher. Library synthesis was performed using NEB Next Ultra RNA library Prep Kit by Novogene  Inc", "etv2^ci32Gt heterozygous and homozygous embryos were obtained from the incross of etv2^ci32Gt+/ ; UAS:GFP carriers. Embryos were incubated at 28 C for 24 hpf stage and at 24 C for 15 somite stage.", "tissue:Whole embryos|line allele:etv2^Gt2A Gal4ci32|genotype:Homozygous|embryo stage:15 somite", "GSM4131105", "GSM4131105: etv2 homo 15som 1; Danio rerio; RNA Seq", "GSM4131105", null, "1", "Bulk RNA was purified using RNA quous 4 PCR kit ThermoFisher. Library synthesis was performed using NEB Next Ultra RNA library Prep Kit by Novogene  Inc", "GEO Accession:GSM4131105", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP226227", null, null, "Gal4_M_15som_1_1.fq.gz Gal4_M_15som_1_2.fq.gz", "fastq fastq", 7603849500.0, 25346165.0, "GSM4131105 r1", "0:150 1:150", "A:2090131691;C:1715529001;G:1749529239;T:2048659569;N:0", 150, 150, null, null, 2090131691, 1715529001, 1749529239, 2048659569, 0, "SRX7023625", "SRS5544401", "SRA982009", "GEO", "Division of Developmental Biology, Cincinnati Children's Hospital Medical Center", 2, 0.93146, 0.93272, 0.09858, 0.10047, 0.71187, 0.7289, 0.47673, 0.4841, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2019-10-18", "Segmentation", "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": ["55353"], "units": {}, "query_ms": 12.345885988906957}