{"database": "metadata", "table": "run_metadata", "rows": [[74122, "SRR23507772", "SRX19401042", "SRS16795999", "SRP423151", "PRJNA936083", "Gene expression profile at single cell level of the enteric nervous system ENS of 5 dpf dpf zebrafish", "GSE225510", "Other", "We used single cell RNA sequencing scRNA seq to characterize the ENS in the zebrafish intestine. Overall design: Zebrafish intestines were manually isolated at 5dpf and dissociated into a single cell suspension. Live  single cells were sorted by Fluorescence activated cell sorting FACS according to the presence or absence of DAPI signal. Sorted cells were processed and analyzed using 10X scRNAseq.", null, "pubmed:37426341", null, "LK1 Gut ZF", "GSM7049686", null, "source name:Whole gut|cell type:Enteric nervous system cells|tissue:Whole gut|line:wt tgphox2bb:GFP|age:5 dpf loc name:missing|collection date:missing", "LK1 Gut ZF", "Cellranger count v 4.0.0 was employed for barcode processing  gene counting and aggregation of the samples Downstream analysis was performed in Seurat v 4.1.1 Assembly: GRCz10 Supplementary files format and content: Tab separated values files and matrix files", "Whole gut", "N/A N/A", "In total 244 intestines of 5 dpf dpf larvae were isolated  cells were dissociated using 2.17mg/mL papain and the live cells were sorted using FACS. Cells were then loaded onto the 10X platform for single cell RNA sequencing. Libraries were made according to the manufacter\u2019s instructions Single Cell three prime v3 chemistry  10x Genomics", "Zebrafish were kept on a 14/10h light/dark cycle. Embryos and larvae were kept in an incubator at 28.5\u00b0C in HEPES buffered E3 medium.", "cell type:Enteric nervous system cells|tissue:Whole gut|line:wt tgphox2bb:GFP|age:5 dpf", "GSM7049686", "GSM7049686: LK1 Gut ZF; Danio rerio; RNA Seq", "GSM7049686 r1", "GSM7049686", "1", "In total 244 intestines of 5 dpf dpf larvae were isolated  cells were dissociated using 2.17mg/mL papain and the live cells were sorted using FACS. Cells were then loaded onto the 10X platform for single cell RNA sequencing. Libraries were made according to the manufacter's instructions Single Cell three prime v3 chemistry  10x Genomics", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP423151", null, "loader:fastq load.py|options:  readTypes=TTB   read1PairFiles=LK1 Gut ZF run2 S8 L002 I1 001.fastq.gz   read2PairFiles=LK1 Gut ZF run2 S8 L002 R1 001.fastq.gz   read3PairFiles=LK1 Gut ZF run2 S8 L002 R2 001.fastq.gz", "LK1_Gut_ZF_run2_S8_L002_I1_001.fastq.gz LK1_Gut_ZF_run2_S8_L002_R1_001.fastq.gz LK1_Gut_ZF_run2_S8_L002_R2_001.fastq.gz", "fastq fastq fastq", 11851111426.0, 93315838.0, "GSM7049686 r2", "0:8 1:28 2:91", "A:2423220506;C:1877745404;G:2011423380;T:2178841059;N:510909", 8, 28, 91, null, 2423220506, 1877745404, 2011423380, 2178841059, 510909, "SRX19401042", "SRS16795999", "SRA1591972", "Clinical, Erasmus MC", "Clinical Genetics, Erasmus MC", 1, 0.94177, null, 0.12005, null, 0.75592, null, 0.50957, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Netherlands", "2023-02-17", "Larval", "Larval", "Gut", "Digestive 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": ["74122"], "units": {}, "query_ms": 14.522710000164807}