{"database": "metadata", "table": "run_metadata", "rows": [[74894, "SRR24100391", "SRX19900530", "SRS17254305", "SRP431420", "PRJNA953151", "To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during trunk development", "GSE229162", "Transcriptome Analysis", "To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during notochord and muscle development. Overall design: Gene expression analysis using RNA seq data from wild type zebrafish embryos and the tpcn2 mutant  each with five biological replicates.", null, "pubmed:38028019", null, "Zebrafish embryos  Strain: ABTU  Stage: 17 18 somite Biol rep 5", "GSM7156158", null, "source name:Whole embryo|tissue:Whole embryo|strain:ABTU|genotype:WT|developmental stage:17 18 somite stage|geo loc name:missing|collection date:missing", "Zebrafish embryos  Strain: ABTU  Stage: 17 18 somite Biol rep 5", "Performed adapter trimming with cutadapt v3.4 software with parameters: \"  minimum length=30  a A\\{100\\}  A A\\{100\\}  a CTGTCTCTTATACACATCT  A CTGTCTCTTATACACATCT  g AGATGTGTATAAGAGACAG  G AGATGTGTATAAGAGACAG\". Read alignment to mm10 using STAR v2.7 aligner with default settings and extra parameters \"  outSAMtype BAM SortedByCoordinate   quantMode GeneCounts\". Gene overlapping read counts and differentially expressed genes were calculated using DEseq2 v1.30.0. Assembly: danRer10 Genome Reference Consortium Zebrafish Build 10 Supplementary files format and content: all.tsv: Tab delimited text file includes raw counts. Supplementary files format and content: Treatment 1 vs Control.diffexp.tsv: Table of differential expression results for per gene calculated with DESeq2.", "Whole embryo", null, "RNA extraction was performed using RNAzol\u00ae according to the manufacturer\u2019s instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.", "Embryos were collected from wild type ABTU and mutant TPC2 fish line and kept at 28 \u00b0C.", "tissue:Whole embryo|strain:ABTU|genotype:WT|developmental stage:17 18 somite stage", "GSM7156158", "GSM7156158: Zebrafish embryos  Strain: ABTU  Stage: 17 18 somite Biol rep 5; Danio rerio; RNA Seq", "GSM7156158 r1", "GSM7156158", "1", "RNA extraction was performed using RNAzol\u00ae according to the manufacturer's instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP431420", null, null, "V300083329_L01_5_1.fq.gz V300083329_L01_5_2.fq.gz", "fastq fastq", 7153463400.0, 35767317.0, "GSM7156158 r1", "0:100 1:100", "A:1958525430;C:1615815830;G:1630221563;T:1948754839;N:145738", 100, 100, null, null, 1958525430, 1615815830, 1630221563, 1948754839, 145738, "SRX19900530", "SRS17254305", "SRA1638521", "Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology", "Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology", 2, 0.90204, 0.9263, 0.09062, 0.09528, 0.72013, 0.71632, 0.49222, 0.48822, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-04-06", "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": ["74894"], "units": {}, "query_ms": 9.73120100388769}