{"database": "metadata", "table": "run_metadata", "rows": [[54191, "SRR10095967", "SRX6828142", "SRS5370317", "SRP221273", "PRJNA564810", "A Single Cell Transcriptome Atlas for Zebrafish Development", "PRJNA564810", "Other", "The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge  we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap  we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore  we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes  including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis  to launch an effort to define the diversity of cell types during zebrafish organogenesis  and to examine the transcriptional profiles that produce each cell type over developmental time.", null, null, null, null, "2a", null, "strain:Tgelavl3:GCaMP6s|age:2 dpf|sex:unknown|tissue:whole embryo|Replicate name:2a|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish embryos", "2a", "2a", "10X v2 chromium cDNA library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP221273", null, "loader:latf load", "2a elav_gcamp_48h_S1_L001_R1_001.fastq elav_gcamp_48h_S1_L001_R2_001.fastq elav_gcamp_48h_S1_L002_R1_001.fastq elav_gcamp_48h_S1_L002_R2_001.fastq elav_gcamp_48h_S1_L003_R1_001.fastq elav_gcamp_48h_S1_L003_R2_001.fastq elav_gcamp_48h_S1_L004_R1_001.fastq elav_gcamp_48h_S1_L004_R2_001.fastq", "fastq fastq fastq fastq fastq fastq fastq fastq fastq", 30654488793.0, 192795527.0, "2a.gz", "0:26 1:133", "A:8922702024;C:6370087682;G:7321183700;T:8019014142;N:21501245", 26, 133, null, null, 8922702024, 6370087682, 7321183700, 8019014142, 21501245, "SRX6828142", "SRS5370317", "SRA960102", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.00427, 0.91705, 0.00106, 0.08701, 0.98999, 0.8198, 0.35255, 0.50555, 26, 133, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "unknown", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-12-10", "Hatching", "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": ["54191"], "units": {}, "query_ms": 14.344003997393884}