{"database": "metadata", "table": "run_metadata", "rows": [[59292, "SRR11811475", "SRX8362742", "SRS6678633", "SRP262311", "PRJNA633835", "Single cell RNA seq and ATAC seq of zebrafish retina", "GSE150839", "Other", "To study the transcriptomic and chromatin accessibility heterogeneity of zebrafish retinal progenitor cells Overall design: 2 retinal samples from embryonic zebrafish", null, "pubmed:32699896", null, "RNA seq retina atoh7 44hpf", "GSM4559534", null, "source name:retina|strain:Tgatoh7:turboGFP dest1::atoh7:gapRFP|tissue:retina|developmental stage:44 hpf", "RNA seq retina atoh7 44hpf", "Raw datasets of single cell RNA seq were aligned zebrafish genome  GRCz10  filtered  and counted using the Cell Ranger software v2.1.0  10x Genomics to generate the processed matrix data. Raw data of single cell ATAC seq were aligned zebrafish genome  GRCz10  filtered  and counted using the Cell Ranger ATAC software v1.1  10x Genomics to generated the processed matrix data. Genome build: GRCz10 Supplementary files format and content: Processed data files are in tar.gz format  containing matrix files for further analysis.", "retina", null, "Zebrafish retina at the desired developmental stages were dissected and dissociated using papain for single cell RNA seq. The single nuclei were further extracted by digitonin for single cell ATAC seq. The libraries were constructed using the Chromium Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x genomics  PN 120237 or the Chromium Single Cell ATAC Library & Gel Bead Kit 10x genomics following the manufacturer\u2019s protocol", null, "strain:Tgatoh7:turboGFP dest1::atoh7:gapRFP|tissue:retina|developmental stage:44 hpf", "GSM4559534", "GSM4559534: RNA seq retina atoh7 44hpf; Danio rerio; RNA Seq", "GSM4559534", null, "1", "Zebrafish retina at the desired developmental stages were dissected and dissociated using papain for single cell RNA seq. The single nuclei were further extracted by digitonin for single cell ATAC seq. The libraries were constructed using the Chromium Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x genomics  PN 120237 or the Chromium Single Cell ATAC Library & Gel Bead Kit 10x genomics following the manufacturer's protocol", "GEO Accession:GSM4559534", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP262311", null, "intentional duplicate|options:  max err count 100000000", "atoh7_scRNA_bam.bam", "10X Genomics bam file", 61111212107.0, 414028035.0, "GSM4559534 r1", "0:147.60", "A:18052310869;C:12727112571;G:14225357068;T:16105981406;N:450193", 147, null, null, null, 18052310869, 12727112571, 14225357068, 16105981406, 450193, "SRX8362742", "SRS6678633", "SRA1077074", "GEO", "Institute of Neuroscience, Chinese Academy of Sciences", 1, 0.89647, null, 0.06712, null, 0.85228, null, 0.50102, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-05-19", "Pharyngula", "Embryo", "Eye", "Sensory 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": ["59292"], "units": {}, "query_ms": 8.50314600393176}