run_metadata: 29142

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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
29142	SRR32025073	SRX27375416	SRS23810880	SRP476805	PRJNA1050594	Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture	GSE249792	Transcriptome Analysis	Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression. In humans loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b / double knockout zebrafish larvae while smad6a / ;smad6b / double knockout zebrafish have a reduced diameter associated with early mortality. Surprisingly the smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish model is viable and survives to maturity although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis and that using the qKO zebrafish model thus far the only known model of aortic dissection and rupture in this species can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools each containing five smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish or wt control cousins. Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10 RNA sequencing was performed on five pools each containing three smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO adult aortas and five pools of three wt control cousins aortas. For quantseq sample 11 20 RNA sequencing was performed on five pools each containing three smad3a / ;smad3b / double knockout DKO zebrafish or wt control cousins. For quantseq sample 21 30 RNA sequencing was performed on five pools each containing three smad6a / ;smad6b / double knockout DKO zebrafish or wt control cousins.				control 3 for smad3abDKO biol rep 1 5 dpf 5 fish pooled	GSM8741279		source name:pool of 3 whole embryos\|tissue:pool of 3 whole embryos\|genotype:wt control\|geo loc name:missing\|collection date:missing	control 3 for smad3abDKO biol rep 1 5 dpf 5 fish pooled	Raw read QC: UMI and spacer were removed using UMI tools v1.1.4 resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample trimmed reads were mapped on the zebrafish genome GRCz11 ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx	pool of 3 whole embryos		For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.	Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf medium was refreshed. For adults zebrafish were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems Tecniplast at a constant temperature 27 28°C pH 7 5 conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.	tissue:pool of 3 whole embryos\|genotype:wt control	GSM8741279	GSM8741279: control 3 for smad3abDKO biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq	GSM8741279 r1	GSM8741279	1	For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ELEMENT	Element AVITI		SRP476805			13_wt_control_E9_R1.fastq.gz	fastq	1500149700.0	20001996.0	GSM8741279 r1	0:75	A:516842151;C:249094684;G:289026249;T:444994403;N:192213	75				516842151	249094684	289026249	444994403	192213	SRX27375416	SRS23810880	SRA2053000	Callewaert Lab, Biomolecular medicine, Ghent University	Callewaert Lab, Biomolecular medicine, Ghent University												B		usable mapping rate	element	element	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown		Belgium	2025-01-16	Multi-stage	Multi-stage	Whole Organism	All anatomical structures