{"database": "metadata", "table": "run_metadata", "rows": [[74461, "SRR23802570", "SRX19634451", "SRS17003621", "SRP426621", "PRJNA943252", "Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail]", "GSE227118", "Other", "We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized  filtered  and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.", "parent bioproject:PRJNA510836", null, null, "Whole tail  72 hpf", "GSM7091920", null, "source name:transgenic zebrafish embryos wild type|tissue:Whole tail|developmental stage:72 hpf", "Whole tail  72 hpf", "the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode", "transgenic zebrafish embryos wild type", "No treatments", "Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", "Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were bisected on the axial plane towards the caudal end of the yolk extension  tail tissues were then homogenized  filtered  and viable cells sorted using live dead staining FACS into PBS  collecting at least 25 000 cells.", "tissue:Whole tail|developmental stage:72 hpf", "GSM7091920", "GSM7091920: Whole tail  72 hpf; Danio rerio; RNA Seq", "GSM7091920 r1", "GSM7091920", "1", "Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP426621", null, null, "EH_Tails_Single_Cell_GAGACGGA_L002.fastq.sorted.fastq.gz", "fastq", 589786185.0, 9927008.0, "GSM7091920 r2", "0:59.41", "A:170171480;C:115960508;G:111370241;T:192283114;N:842", 59, null, null, null, 170171480, 115960508, 111370241, 192283114, 842, "SRX19634451", "SRS17003621", null, null, "Oncology/Hematology, Boston Children's Hospital", 1, 0.88418, null, 0.1452, null, 0.78173, null, 0.48617, null, 61, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2023-03-10", "Larval", "Larval", "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": ["74461"], "units": {}, "query_ms": 11.34278898825869}