{"database": "metadata", "table": "run_metadata", "rows": [[66176, "SRR15931549", "SRX12221647", "SRS10197714", "SRP337628", "PRJNA764222", "Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [scRNA seq]", "GSE184363", "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: 2 samples were analyzed: 1 chd8+/+ wild type and 1 chd8sa19827/sa19827 homogous mutants. Each sample is comprised of dissociated cells from the mid and posterior intestine of 3 adult zebrafish.", "parent bioproject:PRJNA764218", "pubmed:36375841", null, "chd8 KO", "GSM5585126", null, "tissue:Intestinal cells|genotype:chd8 / ", "chd8 KO", "Alignment  barcode and UMI filtering and counting were performed with Cell Ranger 3.1.0 count  using GRCz11 assembly and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Filtered contains only detected cellular barcodes feature barcode matrix each element of the matrix is the number of UMIs associated with a feature row and a barcode column in Market Exchange Format MEX and gzipped. Supplementary files format and content: Gzipped tsv files with feature and barcode sequences corresponding respectively to row and column indices from the matrix.", "Intestinal cells", null, "chd8+/+ and homozygous chd8 sa19827/sa19827 male adult zebrafish were euthanized in 800 \u00b5g/ml tricaine solution. The fish were dissected  their guts were harvested and placed in RPMI at room temperature. The guts were rolled on paper moistened with RPMI to remove the fat residue  then placed in RPMI with 10% fetal calf serum and cut into small pieces that were placed in 1 ml of digestion medium 1 ml of RPMI   12 \u00b5l of activated fetal calf serum   10 mg of dispase collagenase for 15 minutes  at 37 \u00b0C  under agitation at 500 rpm. The cells were then filtered on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  using the plunger of 1 ml syringe. Cell number and viability were determined by a Trypan Blue exclusion assay on a Neubauer Chamber. Samples consisted of > 90 % viable cells were processed on the Chromium Controller from 10X Genomics Leiden  The Netherlands. 10 000 total cells were loaded per well to yield approximately 6 500 captured cells into nanoliter scale Gel Beads in Emulsion GEMs. Single cell 3\u2019 mRNA seq library were generated according to 10X Genomics User Guide for Chromium Single Cell 3\u2019 Reagent Kits v3 Chemistry. Briefly  GEMs were generated by combining barcoded gel beads  a RT master mix containing cells  and partitioning oil onto Chromium Chip B. Following full length cDNA synthesis and barcoding from poly adenylated mRNA  GEMs were broken and pooled before cDNA amplification by PCR using 11 cycles. post enzymatic fragmentation and size selection  sequencing library were constructed by adding Illumina Paris  France P5 and P7 primers as well as sample index via end repair  A tailing  adaptor ligation and PCR with 14 cycles. Library quantification and quality control was performed using Bioanalyzer 2100 Agilent Technologies  Santa Clara CA.", null, "genotype:chd8 / ", "GSM5585126", "GSM5585126: chd8 KO; Danio rerio; RNA Seq", "GSM5585126", null, "1", "chd8+/+ and homozygous chd8 sa19827/sa19827 male adult zebrafish were euthanized in 800 \u00b5g/ml tricaine solution. The fish were dissected  their guts were harvested and placed in RPMI at room temperature. The guts were rolled on paper moistened with RPMI to remove the fat residue  then placed in RPMI with 10% fetal calf serum and cut into small pieces that were placed in 1 ml of digestion medium 1 ml of RPMI   12 \u00b5l of activated fetal calf serum   10 mg of dispase collagenase for 15 minutes  at 37 \u00b0C  under agitation at 500 rpm. The cells were then filtered on a cell filter diameter 40 \u00b5m  Dutscher  ref 141378C  using the plunger of 1 ml syringe. Cell number and viability were determined by a Trypan Blue exclusion assay on a Neubauer Chamber. Samples consisted of > 90 % viable cells were processed on the Chromium Controller from 10X Genomics Leiden  The Netherlands. 10 000 total cells were loaded per well to yield approximately 6 500 captured cells into nanoliter scale Gel Beads in Emulsion GEMs. Single cell three prime mRNA seq library were generated according to 10X Genomics User Guide for Chromium Single Cell three prime Reagent Kits v3 Chemistry. Briefly  GEMs were generated by combining barcoded gel beads  a RT master mix containing cells  and partitioning oil onto Chromium Chip B. Following full length cDNA synthesis and barcoding from poly adenylated mRNA  GEMs were broken and pooled before cDNA amplification by PCR using 11 cycles. post enzymatic fragmentation and size selection  sequencing library were constructed by adding Illumina Paris  France P5 and P7 primers as well as sample index via end repair  A tailing  adaptor ligation and PCR with 14 cycles. Library quantification and quality control was performed using Bioanalyzer 2100 Agilent Technologies  Santa Clara CA.", "GEO Accession:GSM5585126", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP337628", null, null, "GLHT10.R1.fastq.gz GLHT10.R2.fastq.gz", "fastq fastq", 64945652822.0, 391218083.0, "GSM5585126 r1", "0:67.32 1:98.69", "A:18328460514;C:11753978727;G:12225228372;T:22573401879;N:64583330", 67, 98, null, null, 18328460514, 11753978727, 12225228372, 22573401879, 64583330, "SRX12221647", "SRS10197714", "SRA1296109", "GEO", "IGBMC", 2, 0.00942, 0.92207, 0.00301, 0.14877, 0.99324, 0.82416, 0.42574, 0.69119, 28, 96, "T", "B", "sc-like readlen", "illumina", "nextseq", "3prime", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "France", "2021-09-17", "Adult", "Adult", "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": ["66176"], "units": {}, "query_ms": 12.747368004056625}