run_metadata: 66175

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
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		chd8+/+ 4dpf eNCC #2	GSM5585063		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		chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females and the eggs were incubated at 28.5 °C. 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 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g during 2 minutes at room temperature the supernatant was removed and 100 µl of FACS Max medium were added AMSBIO ref T200100. The larval bodies were then placed on a cell filter diameter 40 µm Dutscher ref 141378C previously moistened with 100 µL of FACS Max medium and the cells were filtered using a 1 ml syringe plunger. The filter was rinsed with 400 µl 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 °C in 10 µl of PBS RNAsine 1 U/µl. 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.		genotype:chd8 +/+	GSM5585063	GSM5585063: chd8+/+ 4dpf eNCC #2; Danio rerio; RNA Seq	GSM5585063		1	chd8+/+ and chd8 sa19827/sa19827 males were crossed with Tg2phox2bb:EGFP females and the eggs were incubated at 28.5 °C. 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 µl of inactivated fetal calf serum. The tubes were centrifuged at 2000 g during 2 minutes at room temperature the supernatant was removed and 100 µl of FACS Max medium were added AMSBIO ref T200100. The larval bodies were then placed on a cell filter diameter 40 µm Dutscher ref 141378C previously moistened with 100 µL of FACS Max medium and the cells were filtered using a 1 ml syringe plunger. The filter was rinsed with 400 µl 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 °C in 10 µl of PBS RNAsine 1 U/µl. 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		SRP337626		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				581790111	491684308	500076074	578254560	64847	SRX12221397	SRS10197464	SRA1296090	GEO	IGBMC	1	0.915		0.08656		0.72537		0.52001		50		B		usable mapping rate	illumina	hiseq_era	full_length	cdna_unspecified	nextera	sc	single_cell_plate	smartseq		France	2021-09-17	Larval	Larval	Brain	Nervous System