{"database": "metadata", "table": "run_metadata", "rows": [[33906, "SRR30879300", "SRX26276608", "SRS22814230", "SRP536515", "PRJNA1168532", "scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf", "GSE278733", "Transcriptome Analysis", "The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.", null, null, null, "dsRED+ WT 4 dpf", "GSM8553898", null, "tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT  EK strain|geo loc name:missing|collection date:missing", "dsRED+ WT 4 dpf", "Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3\u2032 gene counting were performed by the standard 10X Genomics\u2019s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics\u2019s CellRanger and visualized using 10X Genomics\u2019s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files", "4 dpf", null, "WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics\u2019s Chromium instrument and Dual index Single Cell 3\u2032 Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer\u2019s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.", null, "tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT  EK strain", "GSM8553898", "GSM8553898: dsRED+ WT 4 dpf; Danio rerio; RNA Seq", "GSM8553898 r1", "GSM8553898", "1", "WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3\u2032 Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP536515", null, "loader:fastq load.py", "WT_dsRED_S1_L003_I1_001.fastq.gz WT_dsRED_S1_L003_I2_001.fastq.gz WT_dsRED_S1_L003_R1_001.fastq.gz WT_dsRED_S1_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 3989006196.0, 28905842.0, "GSM8553898 r3", "0:10 1:10 2:28 3:90", "A:725297656;C:600094089;G:596392169;T:650543321;N:29198545", 10, 10, 28, 90, 725297656, 600094089, 596392169, 650543321, 29198545, "SRX26276608", "SRS22814230", "SRA1985700", "nih", "nih", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-10-03", "Larval", "Larval", "Multi-tissue", "Multi-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": ["33906"], "units": {}, "query_ms": 10.795394999149721}