{"database": "metadata", "table": "run_metadata", "rows": [[29133, "SRR32025064", "SRX27375425", "SRS23810888", "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\u00ae 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.", null, null, null, "control 2 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled", "GSM8741288", null, "source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:wt control|geo loc name:missing|collection date:missing", "control 2 for smad6abDKO  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", null, "For RNA extraction  the Rneasy\u00ae 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\u2019 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\u00b0C 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\u00b0C  pH 7 5  conductivity 550\u00b5S 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", "GSM8741288", "GSM8741288: control 2 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq", "GSM8741288 r1", "GSM8741288", "1", "For RNA extraction  the Rneasy\u00ae 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "22_wt_control_F10_R1.fastq.gz", "fastq", 1283795850.0, 17117278.0, "GSM8741288 r1", "0:75", "A:442456808;C:219464610;G:244269392;T:377385874;N:219166", 75, null, null, null, 442456808, 219464610, 244269392, 377385874, 219166, "SRX27375425", "SRS23810888", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"]], "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": ["29133"], "units": {}, "query_ms": 9.187419993395451}