{"database": "metadata", "table": "run_metadata", "rows": [[66175, "SRR15931294", "SRX12221397", "SRS10197464", "SRP337626", "PRJNA764215", "Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [RNA seq]", "GSE184359", "Transcriptome Analysis", "Individuals with mutations in CHD8 present with gastrointestinal complaints  yet the underlying mechanisms are understudied. Here  utilizing a stable constitutive chd8 mutant zebrafish model  we found that the loss of chd8 leads to reduced number of vagal neural crest cells NCCs  enteric neural and glial progenitors  emigrating from the neural tube and that their early migration capability was altered. At later stages  although the intestinal colonization by the NCCs was complete  we found decreased numbers of both serotonin producing enterochromaffin cells and NCC derived serotonergic neurons  suggesting an intestinal hyposerotonemia in absence of chd8. Further  transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last  single cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8  NCC development  intestinal homeostasis  and autism associated gastrointestinal complaints. Overall design: 8 samples were analyzed: 4 tgphox2bb:GFP;chd8+/+ wild type and 4 tgphox2bb:GFP;chd8sa19827/+ heterozygous mutants. Each sample is comprised of a clutch of at least 80 dpf 4 dpf larvae.", "parent bioproject:PRJNA764218", "pubmed:36375841", null, "chd8+/+ 4dpf eNCC #2", "GSM5585063", null, "tissue:enteric Neural Crest Cells|genotype:chd8 +/+", "chd8+/+ 4dpf eNCC #2", "Base calling : Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14. Alignment : Reads were mapped onto GRCz11 assembly of Danio rerio genome using STAR 2.5.3a. Quantification : Gene expression was quantified using HTSeq v0.6.1p1 and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Tabulated text file containing raw read counts in each sample.", "enteric Neural Crest Cells", null, "chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females  and the eggs were incubated at 28.5 \u00b0C.  At 4 dpf dpf  the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube  all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma  ref 59417C 100ML.  The digestion was stopped post 10 minutes by adding 50 \u00b5l of inactivated fetal calf serum. The tubes were centrifuged at 2000 g  during 2 minutes at room temperature  the supernatant was removed and 100 \u00b5l of FACS Max medium were added AMSBIO  ref T200100.  The larval bodies were then placed on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  previously moistened with 100 \u00b5L of FACS Max medium  and the cells were filtered  using a 1 ml syringe plunger. The filter was rinsed with 400 \u00b5l of FACS Max medium  the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted  using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP positive cells at  80 \u00b0C  in 10 \u00b5l of PBS RNAsine 1 U/\u00b5l. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe  Saint Germain en Laye  France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina  San Diego  CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter  Villepinte  France  the size and concentration of libraries were assessed by capillary electrophoresis.", null, "genotype:chd8 +/+", "GSM5585063", "GSM5585063: chd8+/+ 4dpf eNCC #2; Danio rerio; RNA Seq", "GSM5585063", null, "1", "chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females  and the eggs were incubated at 28.5 \u00b0C.  At 4 dpf dpf  the larvae were euthanized in 2 mg/ml tricaine diluted in RPMI and the heads of the larvae were discarded. The rest of the larval bodies were collected in a 2 ml Eppendorf tube  all RPMI was removed and replaced with 1 ml of Trypsin EDTA 1X Sigma  ref 59417C 100ML.  The digestion was stopped post 10 minutes by adding 50 \u00b5l of inactivated fetal calf serum. The tubes were centrifuged at 2000 g  during 2 minutes at room temperature  the supernatant was removed and 100 \u00b5l of FACS Max medium were added AMSBIO  ref T200100.  The larval bodies were then placed on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  previously moistened with 100 \u00b5L of FACS Max medium  and the cells were filtered  using a 1 ml syringe plunger. The filter was rinsed with 400 \u00b5l of FACS Max medium  the cells were collected and placed in a 1.5 ml Eppendorf tube. The GFP positive cells were immediately sorted  using an ARIA Fusion cell sorter and an excitation wavelength of 488 nm.  We stored the GFP positive cells at  80 \u00b0C  in 10 \u00b5l of PBS RNAsine 1 U/\u00b5l. Full length cDNA were generated directly from 950 to 1300 cells frozen in PBS buffer containing RNAse inhibitor using Clontech SMART Seq v4 Ultra Low Input RNA kit for Sequencing Takara Bio Europe  Saint Germain en Laye  France according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq Amp polymerase. 600 pg of pre amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit 96 samples Illumina  San Diego  CA followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads Beckman Coulter  Villepinte  France  the size and concentration of libraries were assessed by capillary electrophoresis.", "GEO Accession:GSM5585063", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP337626", null, "loader:fastq load.py", "GLHT2.fastq.gz", "fastq", 2151869900.0, 43037398.0, "GSM5585063 r1", "0:50", "A:581790111;C:491684308;G:500076074;T:578254560;N:64847", 50, null, null, null, 581790111, 491684308, 500076074, 578254560, 64847, "SRX12221397", "SRS10197464", "SRA1296090", "GEO", "IGBMC", 1, 0.915, null, 0.08656, null, 0.72537, null, 0.52001, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "France", "2021-09-17", "Larval", "Larval", "Brain", "Nervous 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": ["66175"], "units": {}, "query_ms": 9.477450003032573}