run_metadata: 66176

This data as json

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
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		chd8 KO	GSM5585126		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		chd8+/+ and homozygous chd8 sa19827/sa19827 male adult zebrafish were euthanized in 800 µg/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 µl of activated fetal calf serum 10 mg of dispase collagenase for 15 minutes at 37 °C under agitation at 500 rpm. The cells were then filtered on a cell filter diameter 40 µm 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’ mRNA seq library were generated according to 10X Genomics User Guide for Chromium Single Cell 3’ 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.		genotype:chd8 /	GSM5585126	GSM5585126: chd8 KO; Danio rerio; RNA Seq	GSM5585126		1	chd8+/+ and homozygous chd8 sa19827/sa19827 male adult zebrafish were euthanized in 800 µg/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 µl of activated fetal calf serum 10 mg of dispase collagenase for 15 minutes at 37 °C under agitation at 500 rpm. The cells were then filtered on a cell filter diameter 40 µm 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		SRP337628			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			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		France	2021-09-17	Adult	Adult	Gut	Digestive System