{"database": "metadata", "table": "run_metadata", "rows": [[63042, "SRR13565184", "SRX9963428", "SRS8137095", "SRP303506", "PRJNA695274", "Single cell response landscape of graded Nodal signaling  in zebrafish explants [single cell RNA seq]", "GSE165653", "Transcriptome Analysis", "Purpose: To construct cell landscape of graded Nodal signaling  in zebrafish explants. Methods:  Nodal injected explants injected with 10pg ndr2 mRNA were harvested at xxxhpf  5hpf  6hpf  8hpf  10hpf  24hpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics  PN 120237 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 42 317 single cell transcriptomes were collected post stringent quality control measures. Conclusions: 19 Cell types from 6 developmental stages were identified  Nodal explant mainly contains the axial mesoderm prechordal plate and notochord and anterior posterior patterned head structures. Overall design: zebrafish explants injected with 10pg ndr2 mRNA were harvested at xxxhpf  5hpf  6hpf  8hpf  10hpf  24hpf for scRNA seq.", "parent bioproject:PRJNA695267", "pubmed:37729057", null, "zebrafish Nodal explants 5hpf", "GSM5047612", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:5hpf|treatment:injected with 10pg ndr2 mRNA", "zebrafish Nodal explants 5hpf", "Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 or GRCz10 using the 10x Genomics CellRanger pipeline version 2.1.1 with default parameters. Genome build: GRCz11/GRCz10 Supplementary files format and content: tar compressed  files included filtered gene bc matrices post running CellRanger pipeline", "zebrafish cells", "10pg of ndr2 mRNA 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 4hpf  5hpf  6hpf  8hpf  10hpf and 24hpf corresponding to embryonic developmental stage separately.", "Libraries were prepared using Chromium Controller and Chromium Single Cell 3\u2019Library & Gel Bead Kit v2 10x Genomics  PN 120237 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:5hpf|treatment:injected with 10pg ndr2 mRNA", "GSM5047612", "GSM5047612: zebrafish Nodal explants 5hpf; Danio rerio; RNA Seq", "GSM5047612", null, "1", "Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v2 10x Genomics  PN 120237 according to the manufacturer's protocol for 10000 cells recovery.", "GEO Accession:GSM5047612", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP303506", null, null, "wt_cyc_5hpf_S1_L002_R1_001.fastq.gz wt_cyc_5hpf_S1_L002_R2_001.fastq.gz", "fastq fastq", 132074187896.0, 437331748.0, "GSM5047612 r1", "0:151 1:151", "A:33956635680;C:22833737374;G:24573359678;T:50703117357;N:7337807", 151, 151, null, null, 33956635680, 22833737374, 24573359678, 50703117357, 7337807, "SRX9963428", "SRS8137095", "SRA1188621", "GEO", "Institute of genetics, Zhejiang University", 2, 0.25456, 0.90744, 0.02797, 0.06895, 0.96999, 0.79732, 0.57673, 0.63217, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-01-27", "Blastula", "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": ["63042"], "units": {}, "query_ms": 7.817841003998183}