{"database": "metadata", "table": "run_metadata", "rows": [[33420, "SRR30186675", "SRX25652378", "SRS22295179", "SRP525362", "PRJNA1146366", "Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level", "GSE274407", "Transcriptome Analysis", "Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.", null, "pubmed:39642879", null, "ENS5dpf", "GSM8448585", null, "source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf|geo loc name:missing|collection date:missing", "ENS5dpf", "The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files", "intestine", null, "To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer\u2019s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf", "GSM8448585", "GSM8448585: ENS5dpf; Danio rerio; RNA Seq", "GSM8448585 r1", "GSM8448585", "1", "To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP525362", null, "loader:fastq load.py", "FT-SA26636_S4_L006_I1_001.fastq.gz FT-SA26636_S4_L006_R1_001.fastq.gz FT-SA26636_S4_L006_R2_001.fastq.gz", "fastq fastq fastq", 22493595040.0, 72559984.0, "GSM8448585 r2", "0:8 1:151 2:151", "A:5532271824;C:3275587569;G:3623404196;T:9478183540;N:3668039", 8, 151, 151, null, 5532271824, 3275587569, 3623404196, 9478183540, 3668039, "SRX25652378", "SRS22295179", "SRA1943746", "Bronner lab, Biology and Biological Engineering, Caltech", "Bronner lab, Biology and Biological Engineering, Caltech", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-09", "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": ["33420"], "units": {}, "query_ms": 8.643577002658276}