{"database": "metadata", "table": "run_metadata", "rows": [[63471, "SRR13839965", "SRX10218346", "SRS8362929", "SRP309047", "PRJNA706197", "scRNA seq timeline of first pharyngeal arch migratory stream in zebrafish", "GSE168133", "Transcriptome Analysis", "We have performed single cell RNA seq of cranial NC cells in zebrafish over several stages during their migration Overall design: single cells were captured via FACS and 10X Chromium platform at 6 stages across neural crest migration.", "parent bioproject:PRJNA706402", "pubmed:34936864", null, "FACS sorted NC cells 20 hpf", "GSM5129556", null, "tissue:FACS sorted sox10:nEOS cells|genotype:Tgsox10:nEOSw18|age:20 hpf|cell type:NC cell", "FACS sorted NC cells 20 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: aggregated.arch.counts.matrix.csv and 18hpf.counts.matrix.csv contain counts matrix for each cell that met quality thresholds.  In aggregated.arch.counts.matrix.csv  barcode.1 corresponds to \"Sample 1\"  barcode.2 corresponds to \"Sample 2\"  and so on.", "FACS sorted sox10:nEOS cells", null, "Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7  which used chemistry v3", null, "genotype:Tgsox10:nEOSw18|age:20 hpf|cell type:NC cell", "GSM5129556", "GSM5129556: FACS sorted NC cells 20 hpf; Danio rerio; RNA Seq", "GSM5129556", null, "1", "Embryos were imaged on a Nikon confocal and NC cells were photoconverted prior to dissociation using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromiium chemistry v2 except Sample 7  which used chemistry v3", "GEO Accession:GSM5129556", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP309047", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=Arch 1 20hpf S1 L001 I1 001.fastq.gz   read2PairFiles=Arch 1 20hpf S1 L001 R1 001.fastq.gz   read3PairFiles=Arch 1 20hpf S1 L001 R2 001.fastq.gz", "Arch_1_20hpf_S1_L001_I1_001.fastq.gz Arch_1_20hpf_S1_L001_R1_001.fastq.gz Arch_1_20hpf_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 9657625956.0, 73163833.0, "GSM5129556 r1", "0:8 1:26 2:98", "A:2830411224;C:1999540517;G:2299090795;T:2527252325;N:1331095", 8, 26, 98, null, 2830411224, 1999540517, 2299090795, 2527252325, 1331095, "SRX10218346", "SRS8362929", "SRA1202350", "GEO", "Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine", 1, 0.93617, null, 0.06368, null, 0.82791, null, 0.51358, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-03-03", "Segmentation", "Embryo", "Embryo Imprecise", "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": ["63471"], "units": {}, "query_ms": 10.99598701694049}