{"database": "metadata", "table": "run_metadata", "rows": [[72834, "SRR23210473", "SRX19158410", "SRS16570831", "SRP418915", "PRJNA927004", "Differential Nodal level promotes mesendoderm cell fate segregation mediated by chromatin organization", "GSE223636", "Other", "Purpose: To investigate the mechanism of prechordal plate and anterior endoderm separation . Methods:  Nodal injected explants injected with 10pg ndr2 mRNA constructed from lft1 mutants and ndr1 morphants 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. For single cell multiomics  zebrafish embryos at 6 hpf were harvested.  Libraries were prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics  4 rxns PN 1000285 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 10 614 single cell transcriptomes and 4 335 multiomics were collected post stringent quality control measures. Conclusions: A slight bias in Nodal signaling promotes a differential chromatin structure between prechordal plate and endoderm  which drives a differential expression of those key regulators  such as gsc and ripply1 in these two cell lineages  and further regulates mesendoderm cell fate separation. Overall design: zebrafish Nodal explants constructed from lft1 mutants and ndr1 morphants were harvested at 6hpf for scRNA seq. Zebrafish embryos were harvested at 6hpf for single cell multiomics.", null, null, null, "zebrafish Nodal explants constructed from ndr1 morphants", "GSM6969676", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf", "zebrafish Nodal explants constructed from ndr1 morphants", "Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 using the 10x Genomics CellRanger pipeline version 6.1.2 and cellranger arc version 2.0.0 with default parameters. Assembly: GRCz11 Supplementary files format and content: tar archivr or  gzip compressed  files included filtered gene bc matrices and ATAC fragments  post running CellRanger or cellranger arc 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 6hpf corresponding to embryonic developmental stage.", "Libraries were prepared using Chromium Controller and Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 10x Genomics  PN 1000075 and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics  4 rxns PN 1000285 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:6hpf", "GSM6969676", "GSM6969676: zebrafish Nodal explants constructed from ndr1 morphants; Danio rerio; RNA Seq", "GSM6969676 r1", "GSM6969676", "1", "Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics  PN 1000075 and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics  4 rxns PN 1000285 according to the manufacturer's protocol for 10000 cells recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP418915", null, null, "ndr1Mo_cyc_6hpf_S5_L002_R1_001.fastq.gz ndr1Mo_cyc_6hpf_S5_L002_R2_001.fastq.gz", "fastq fastq", 82246861872.0, 464671536.0, "GSM6969676 r1", "0:26 1:151", "A:23306781803;C:17200141798;G:18609129782;T:23129217367;N:1591122", 26, 151, null, null, 23306781803, 17200141798, 18609129782, 23129217367, 1591122, "SRX19158410", "SRS16570831", "SRA1581154", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.00753, 0.93187, 0.00244, 0.09764, 0.9867, 0.79813, 0.42974, 0.53736, 26, 151, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-01-24", "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": ["72834"], "units": {}, "query_ms": 23.451097003999166}