{"database": "metadata", "table": "run_metadata", "rows": [[66225, "SRR16148351", "SRX12433217", "SRS10400585", "SRP339629", "PRJNA767802", "RNA seq and ATAC seq of WT and Gli3 /  zebrafish", "PRJNA767802", "Other", "WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 /  replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.", null, null, "Replicate 3  RNAseq WT", null, "RNAseq WT 3", null, "strain:WT3|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: WT EGFP cells", "3", "3", "Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly  the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged  and the supernatant was recovered to a new tube. 0.2 ml chloroform was added  vigorously vortexed  and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol  kept for 10 minutes at room temperature  and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA  USA  converted to sequencing library  and sequenced.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP339629", null, "assembly:GRCz11", "Gli3WT3_aligned.sorted.bam", "bam", 6055778800.0, 30391313.0, "Gli3WT3 aligned.sorted.bam", "0:99.60 1:99.66", "A:1632778751;C:1402895889;G:1402788250;T:1617315910;N:0", 99, 99, null, null, 1632778751, 1402895889, 1402788250, 1617315910, 0, "SRX12433217", "SRS10400585", "SRA1303956", "Rutgers University|Genetics", "Rutgers University", 2, 0.95971, 0.96273, 0.09206, 0.09219, 0.72458, 0.72391, 0.55162, 0.55278, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-10-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"]], "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": ["66225"], "units": {}, "query_ms": 8.330646000104025}