{"database": "metadata", "table": "run_metadata", "rows": [[48049, "SRR6956073", "SRX3899096", "SRS3136393", "SRP137889", "PRJNA449093", "10x analysis of wild type TLAB and MZoep zebrafish embryos at 6 somite stage", "GSE112824", "Transcriptome Analysis", "Wild type and MZoep zebrafish embryos were mechanically dissociated and profiled using 10x Genomics pipeline. Overall design: 10x scRNA seq was performed on visually staged  mechanically dissociated embryos. Samples were combined and sequenced in one batch.", "parent bioproject:PRJNA417291", "pubmed:29700225", null, "WT zebrafish embryo 6 somite", "GSM3084402", null, "tissue:Wild type TLAB Embryo|genotype/variation:wild type TLAB|developmental stage:6 somite|hpf", "WT zebrafish embryo 6 somite", "Data was processed using Cell Ranger 2.0.2  following the pipeline posted on 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. Command \"cellranger mkfastq\" was called to generate demultiplexed FASTQ files from the Illumina BCL output files. Command \"cellranger count\" was used to align the reads to generate the bam files provided as raw data. Single cell gene barcode counts were calculated by \"cellranger count\"  and were filtered to eliminate non cellular barcodes filtered gene barcode counts are provided as processed data. Genome build: dr82 Supplementary files format and content: Compressed folder containing filtered gene barcode matrices in Market Exchange Format MEX  as outputted by \"cellranger count\".", "Wild type TLAB Embryo", null, "Embryos were dechorionated and deyolked manually  mechanically dissociated  washed and resuspended in PBS + 0.1% BSA + 20% Optiprep  filtered through a cell sieve  and encapsulated and lysed in droplets using the 10X Chromium controller. Libraries were prepared using the 10X Chromium Single Cell three prime Reagent Kit. Libraries for the two genotypes were prepared separately to incorporate different read indices. Libraries were pooled together and sequenced in one batch.", "Wild type Tupful longfin / AB or MZoep tz57 fish were incrossed  embryos were collected and grown at 28\u00b0C in chorions until they reached the desired stage confirmed via visual morphological staging.", "genotype/variation:wild type TLAB|developmental stage:6 somite|hpf", "GSM3084402", "GSM3084402: WT zebrafish embryo 6 somite; Danio rerio; RNA Seq", "GSM3084402", null, "1", "Embryos were dechorionated and deyolked manually  mechanically dissociated  washed and resuspended in PBS + 0.1% BSA + 20% Optiprep  filtered through a cell sieve  and encapsulated and lysed in droplets using the 10X Chromium controller. Libraries were prepared using the 10X Chromium Single Cell three prime Reagent Kit. Libraries for the two genotypes were prepared separately to incorporate different read indices. Libraries were pooled together and sequenced in one batch.", "GEO Accession:GSM3084402", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP137889", null, "dangling references:treat as unmapped", "10xWT6S_possorted_genome_bam.bam", "10X Genomics bam file", 9353929816.0, 161274652.0, "GSM3084402 r1", "0:58", "A:2687281275;C:1909606804;G:2337322093;T:2396497626;N:23222018", 58, null, null, null, 2687281275, 1909606804, 2337322093, 2396497626, 23222018, "SRX3899096", "SRS3136393", "SRA683448", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.94618, null, 0.07281, null, 0.8435, null, 0.501, null, 58, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2018-04-06", "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": ["48049"], "units": {}, "query_ms": 9.918771000229754}