{"database": "metadata", "table": "run_metadata", "rows": [[72588, "SRR22797023", "SRX18756814", "SRS16192272", "SRP413556", "PRJNA913420", "Nodal coordinates the anterior posterior patterning of germ layers and induces head formation in zebrafish explants.", "GSE221220", "Other", "Purpose: To investingate cell types in wild type zebrafish explants. Methods:  Wild type explants injected with phenol red were harvested at xxxhpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics  PN 1000075 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 9 968 single cell transcriptomes were collected post stringent quality control measures. Conclusions: 6 Cell types  were identified  wild type explants mainly contains the anterior neural ectoderm and epidermis at 10 hpf. Overall design: Wild type zebrafish explants were harvested at 10hpf for scRNA seq.", null, "pubmed:37729057", null, "zebrafish wild type explant 10hpf", "GSM6856370", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:10hpf|genotype:wild type", "zebrafish wild type explant 10hpf", "Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 Supplementary files format and content: tar compressed  files included filtered gene bc matrices post running CellRanger pipeline", "zebrafish cells", "phenol red was injected to one cell of embryonic animal pole at xxx cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage  then  were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 10hpfcorresponding to embryonic developmental stage separately.", "Libraries were prepared using Chromium Controller and Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 10x Genomics  PN 1000075 according to the manufacturer\u2019s protocol for 10000 cells recovery.", "explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:AB|tissue:embryonic cells|age:10hpf|genotype:wild type", "GSM6856370", "GSM6856370: zebrafish wild type explant 10hpf; Danio rerio; RNA Seq", "GSM6856370 r1", "GSM6856370", "1", "Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics  PN 1000075 according to the manufacturer's protocol for 10000 cells recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP413556", null, "loader:fastq load.py", "WT_10hpf_S1_L001_R1_001.fastq.gz WT_10hpf_S1_L001_R2_001.fastq.gz", "fastq fastq", 144284560800.0, 480948536.0, "GSM6856370 r1", "0:150 1:150", "A:61459567540;C:25433070866;G:24459703281;T:32928214337;N:4004776", 150, 150, null, null, 61459567540, 25433070866, 24459703281, 32928214337, 4004776, "SRX18756814", "SRS16192272", "SRA1561216", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.0, 0.92423, 0.0, 0.16334, 1.0, 0.78228, null, 0.51889, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-12-17", "Gastrula", "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": ["72588"], "units": {}, "query_ms": 26.056843002152164}