{"database": "metadata", "table": "run_metadata", "rows": [[76532, "SRR25081951", "SRX20835391", "SRS18112575", "SRP446710", "PRJNA987386", "Single nucleus chromatin landscapes during zebrafish early embryogenesis", "PRJNA987386", "Other", "Vertebrate embryogenesis is a remarkable process  during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis regulatory elements CREs and gene expression within the hierarchy of cell fate decisions. Here  we employed single nucleus ATAC seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis  including 3.3 hpf  5.25 hpf  6 hpf  10 hpf  12 hpf  18 hpf and 24 hpf  obtained 51 620 high quality nuclei and 23 clusters. Furthermore  by integrating snATAC seq data with single cell RNA seq data  we described the dynamics of chromatin accessibility and gene expression across developmental time points  which validates the accuracy of the chromatin landscape data. Together  our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.", null, null, null, "6 hpf embryos", "scRNA zf6hpf 2", null, "strain:AB/Wild type|isolate:scRNA zf6hpf 2|breed:not collected|cultivar:not collected|ecotype:not determined|age:embryo|dev stage:6 hpf|collection date:2021 08 08|geo loc name:China: Wuhan|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA 6 hpf", "scRNA 6 hpf rep2 oligo", "scRNA 6 hpf rep2 oligo", "scRNA seq of 6 hpf embryos", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP446710", null, "CNGB Experiment ID:CNX0591993", "DP8450003515BR_L01_5_1.fq.gz DP8450003515BR_L01_5_2.fq.gz", "fastq fastq", 14588474300.0, 291769486.0, "DP8450003515BR L01 5 1.fq.gz", "0:20 1:30", "A:3813233297;C:3660627848;G:3388591530;T:3724524333;N:1497292", 20, 30, null, null, 3813233297, 3660627848, 3388591530, 3724524333, 1497292, "SRX20835391", "SRS18112575", "SRA1664681", "BGI Research, Shenzhen", "BGI Research, Shenzhen CNGB Nucleotide Sequence Archive (CNSA) BGI-Shenzhen", 2, 0.00464, 0.0003, 0.00396, 0.00028, 0.9978, 0.99995, 0.39694, 0.5, 20, 30, "T", "T", "mates < 9% mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2023-06-30", "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": ["76532"], "units": {}, "query_ms": 6.897148996358737}