{"database": "metadata", "table": "run_metadata", "rows": [[63868, "SRR14143481", "SRX10512841", "SRS8636598", "SRP313475", "PRJNA719789", "scRNA seq of tailbud development in zebrafish", "GSE171482", "Other", "We have performed single cell RNA seq of whole tailbuds in WT zebrafish at 16 hpf. Overall design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.", null, null, null, "Tailbud single cells at 16 hpf", "GSM5226215", null, "source name:Dissociated tailbuds from 30 hpf 16 hpf embryos|transgenic:AB wildtypes|age:16 hpf embryo|tissue:dissociated tailbuds", "Tailbud single cells at 16 hpf", "FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: .csv file contains counts matrix for each cell that met quality thresholds", "Dissociated tailbuds from 30 hpf 16 hpf embryos", null, "Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7  which used chemistry v3", null, "transgenic:AB wildtypes|age:16 hpf embryo|tissue:dissociated tailbuds", "GSM5226215", "GSM5226215: Tailbud single cells at 16 hpf; Danio rerio; RNA Seq", "GSM5226215", null, "1", "Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7  which used chemistry v3", "GEO Accession:GSM5226215", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP313475", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=WT tailbud S4 L003 I1 001.fastq.gz   read2PairFiles=WT tailbud S4 L003 R1 001.fastq.gz   read3PairFiles=WT tailbud S4 L003 R2 001.fastq.gz", "WT_tailbud_S4_L003_I1_001.fastq.gz WT_tailbud_S4_L003_R1_001.fastq.gz WT_tailbud_S4_L003_R2_001.fastq.gz", "fastq fastq fastq", 30944524598.0, 243657674.0, "GSM5226215 r4", "0:8 1:28 2:91", "A:8382983101;C:6979019830;G:7383731031;T:8197465285;N:1325351", 8, 28, 91, null, 8382983101, 6979019830, 7383731031, 8197465285, 1325351, "SRX10512841", "SRS8636598", "SRA1215249", "GEO", "Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine", 1, 0.94927, null, 0.12443, null, 0.79316, null, 0.48307, null, 91, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-04-05", "Segmentation", "Embryo", "Tail", "Multi-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": ["63868"], "units": {}, "query_ms": 9.627895007724874}