{"database": "metadata", "table": "run_metadata", "rows": [[35822, "SRR33048252", "SRX28313561", "SRS24652526", "SRP577496", "PRJNA1248508", "Transcriptome sequencing of hepatocytes with or without xxx during liver development in zebrafish", "PRJNA1248508", "Other", "The hepatocytes and non hepatocytes within the livers of 3dpf  7 dpf  and adult transgenic Tgfabp10:GFP zebrafish were utilized for experimentation. Upon cessation of opercular movements  animals were euthanized via immersion in ice cold water for ten minutes. In this transgenic line  hepatocytes in the liver express GFP. Subsequently  liver tissues were subjected to enzymatic digestion using 1 mg Collagenase IV dissolved in 1 ml L 15 medium  incubated at room temperature for 20 minutes. Liver tissues were then transferred to Leibovitz L 15 medium with an osmolarity of 300 mOsm and pH adjusted to 7.35. Hepatocytes and non  hepatocytes were isolated through gentle trituration. The chamber was mounted onto the stage of an Olympus inverted microscope equipped with fluorescence capabilities  perfused with fresh L 15 medium for 5 minutes to rinse off debris. Calibrate flow cytometer Moflo XDP  Beckman  ensuring that the instrument settings such as voltage thresholds and compensation matrices are properly configured for GFP detection. Use beads calibrated for green fluorescent protein to adjust the photomultiplier tube voltages and other parameters. Prepare sterile sorting tubes filled with a suitable buffer to collect sorted cells. Pre chill if necessary. Use an argon laser typically at 488 nm for GFP excitation. Set appropriate filters to detect GFP emission  usually centred around 530 nm. Discriminate intact cells from cell fragments based on size and internal complexity. Balance purity and yield by adjusting sort speed and stringency of gating parameters. Follow strict cleaning protocols post sorting to avoid contamination. Isolated cells were collected utilizing flow cytometry  enabling precise sorting of GFP positive hepatocytes from GFP negative non hepatocytes. Approximately 400 hepatocytes and non hepatocytes were harvested from around 12 zebrafish  with 3 replicates per sample. The careful isolation procedures and subsequent sorting by flow cytometry facilitated acquisition of pure populations of hepatocytes and non hepatocytes  ensuring gene expression profiles and reliable downstream analyses of cellular composition.", null, null, null, "D3 GFP", "The hepatocytes within the liver of 3dpf transgenic Tgfabp10:GFP zebrafish", null, "strain:not applicable|isolate:not applicable|breed:hepatocytes|cultivar:transgenic Tgfabp10:GFP zebrafish|ecotype:not applicable|age:not collected|dev stage:3 dpf date:2019 06 19|geo loc name:China: Sichuan|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D3 GFP", "ED19155403", "ED19155403", "library preparations were sequenced on an Illumina Novaseq platform and 150bp paired end reads were generated", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP577496", null, null, "D3_GFP_R1.fq.gz D3_GFP_R2.fq.gz", "fastq fastq", 5675477100.0, 18918257.0, "D3 GFP R1.fq.gz", "0:150 1:150", "A:1686172751;C:1174770916;G:1187685676;T:1626795743;N:52014", 150, 150, null, null, 1686172751, 1174770916, 1187685676, 1626795743, 52014, "SRX28313561", "SRS24652526", "SRA2109063", "Chengdu Medical College|School of Basic Medicine", "Chengdu Medical College", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-04-09", "Larval", "Larval", "Liver", "Liver and Biliary 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": ["35822"], "units": {}, "query_ms": 10.893241997109726}