{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.platform = \"ELEMENT\"", "rows": [[29125, "SRR32025056", "SRX27375433", "SRS23810897", "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, "smad6ab DKO 5 biol rep 1 5 dpf 5 fish pooled", "GSM8741296", null, "source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad6a/b DKO|geo loc name:missing|collection date:missing", "smad6ab DKO 5 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:smad6a/b DKO", "GSM8741296", "GSM8741296: smad6ab DKO 5 biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq", "GSM8741296 r1", "GSM8741296", "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, "30_smad6a__smad6b__F11_R1.fastq.gz", "fastq", 1783531650.0, 23780422.0, "GSM8741296 r1", "0:75", "A:612499747;C:307171870;G:341630182;T:521913046;N:316805", 75, null, null, null, 612499747, 307171870, 341630182, 521913046, 316805, "SRX27375433", "SRS23810897", "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"], [29126, "SRR32025057", "SRX27375432", "SRS23810896", "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, "smad6ab DKO 4 biol rep 1 5 dpf 5 fish pooled", "GSM8741295", null, "source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad6a/b DKO|geo loc name:missing|collection date:missing", "smad6ab DKO 4 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:smad6a/b DKO", "GSM8741295", "GSM8741295: smad6ab DKO 4 biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq", "GSM8741295 r1", "GSM8741295", "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, "29_smad6a__smad6b__E11_R1.fastq.gz", "fastq", 1806895725.0, 24091943.0, "GSM8741295 r1", "0:75", "A:610799963;C:310255661;G:349091544;T:536431072;N:317485", 75, null, null, null, 610799963, 310255661, 349091544, 536431072, 317485, "SRX27375432", "SRS23810896", "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"], [29127, "SRR32025058", "SRX27375431", "SRS23810895", "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, "smad6ab DKO 3 biol rep 1 5 dpf 5 fish pooled", "GSM8741294", null, "source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad6a/b DKO|geo loc name:missing|collection date:missing", "smad6ab DKO 3 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:smad6a/b DKO", "GSM8741294", "GSM8741294: smad6ab DKO 3 biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq", "GSM8741294 r1", "GSM8741294", "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, "28_smad6a__smad6b__D11_R1.fastq.gz", "fastq", 1236162375.0, 16482165.0, "GSM8741294 r1", "0:75", "A:417424019;C:209354549;G:238058828;T:371172361;N:152618", 75, null, null, null, 417424019, 209354549, 238058828, 371172361, 152618, "SRX27375431", "SRS23810895", "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"], [29128, "SRR32025059", "SRX27375430", "SRS23810893", "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, "smad6ab DKO 2 biol rep 1 5 dpf 5 fish pooled", "GSM8741293", null, "source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad6a/b DKO|geo loc name:missing|collection date:missing", "smad6ab DKO 2 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:smad6a/b DKO", "GSM8741293", "GSM8741293: smad6ab DKO 2 biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq", "GSM8741293 r1", "GSM8741293", "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, "27_smad6a__smad6b__C11_R1.fastq.gz", "fastq", 1239721050.0, 16529614.0, "GSM8741293 r1", "0:75", "A:422806413;C:210247744;G:238495376;T:367964420;N:207097", 75, null, null, null, 422806413, 210247744, 238495376, 367964420, 207097, "SRX27375430", "SRS23810893", "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"], [29129, "SRR32025060", "SRX27375429", "SRS23810894", "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, "smad6ab DKO 1 biol rep 1 5 dpf 5 fish pooled", "GSM8741292", null, "source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad6a/b DKO|geo loc name:missing|collection date:missing", "smad6ab DKO 1 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:smad6a/b DKO", "GSM8741292", "GSM8741292: smad6ab DKO 1 biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq", "GSM8741292 r1", "GSM8741292", "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, "26_smad6a__smad6b__B11_R1.fastq.gz", "fastq", 1771498800.0, 23619984.0, "GSM8741292 r1", "0:75", "A:600616051;C:303681611;G:340472236;T:526419468;N:309434", 75, null, null, null, 600616051, 303681611, 340472236, 526419468, 309434, "SRX27375429", "SRS23810894", "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"], [29130, "SRR32025061", "SRX27375428", "SRS23810892", "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 5 for smad6abDKO biol rep 1 5 dpf 5 fish pooled", "GSM8741291", 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 5 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", "GSM8741291", "GSM8741291: control 5 for smad6abDKO biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq", "GSM8741291 r1", "GSM8741291", "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, "25_wt_control_A11_R1.fastq.gz", "fastq", 1574255025.0, 20990067.0, "GSM8741291 r1", "0:75", "A:544358067;C:268587913;G:299883067;T:461155939;N:270039", 75, null, null, null, 544358067, 268587913, 299883067, 461155939, 270039, "SRX27375428", "SRS23810892", "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"], [29131, "SRR32025062", "SRX27375427", "SRS23810891", "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 4 for smad6abDKO biol rep 1 5 dpf 5 fish pooled", "GSM8741290", 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 4 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", "GSM8741290", "GSM8741290: control 4 for smad6abDKO biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq", "GSM8741290 r1", "GSM8741290", "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, "24_wt_control_H10_R1.fastq.gz", "fastq", 1197613800.0, 15968184.0, "GSM8741290 r1", "0:75", "A:413692477;C:202818991;G:227848971;T:353083087;N:170274", 75, null, null, null, 413692477, 202818991, 227848971, 353083087, 170274, "SRX27375427", "SRS23810891", "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"], [29132, "SRR32025063", "SRX27375426", "SRS23810890", "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 3 for smad6abDKO biol rep 1 5 dpf 5 fish pooled", "GSM8741289", 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 3 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", "GSM8741289", "GSM8741289: control 3 for smad6abDKO biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq", "GSM8741289 r1", "GSM8741289", "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, "23_wt_control_G10_R1.fastq.gz", "fastq", 1433154750.0, 19108730.0, "GSM8741289 r1", "0:75", "A:493379384;C:244908245;G:274361129;T:420258548;N:247444", 75, null, null, null, 493379384, 244908245, 274361129, 420258548, 247444, "SRX27375426", "SRS23810890", "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"], [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"], [29134, "SRR32025065", "SRX27375424", "SRS23810889", "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 1 for smad6abDKO biol rep 1 5 dpf 5 fish pooled", "GSM8741287", 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 1 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", "GSM8741287", "GSM8741287: control 1 for smad6abDKO biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq", "GSM8741287 r1", "GSM8741287", "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, "21_wt_control_E10_R1.fastq.gz", "fastq", 1620787500.0, 21610500.0, "GSM8741287 r1", "0:75", "A:556979571;C:275622807;G:309210789;T:478725788;N:248545", 75, null, null, null, 556979571, 275622807, 309210789, 478725788, 248545, "SRX27375424", "SRS23810889", "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"], [29135, "SRR32025066", "SRX27375423", "SRS23810887", "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, "smad3ab DKO 5 biol rep 1 5 dpf 5 fish pooled", "GSM8741286", null, "source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad3a/b DKO|geo loc name:missing|collection date:missing", "smad3ab DKO 5 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:smad3a/b DKO", "GSM8741286", "GSM8741286: smad3ab DKO 5 biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq", "GSM8741286 r1", "GSM8741286", "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, "20_smad3a__smad3b__D10_R1.fastq.gz", "fastq", 1664067900.0, 22187572.0, "GSM8741286 r1", "0:75", "A:575504153;C:284148304;G:316755855;T:487400701;N:258887", 75, null, null, null, 575504153, 284148304, 316755855, 487400701, 258887, "SRX27375423", "SRS23810887", "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"], [29136, "SRR32025067", "SRX27375422", "SRS23810886", "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, "smad3ab DKO 4 biol rep 1 5 dpf 5 fish pooled", "GSM8741285", null, "source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad3a/b DKO|geo loc name:missing|collection date:missing", "smad3ab DKO 4 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:smad3a/b DKO", "GSM8741285", "GSM8741285: smad3ab DKO 4 biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq", "GSM8741285 r1", "GSM8741285", "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, "19_smad3a__smad3b__C10_R1.fastq.gz", "fastq", 1277250825.0, 17030011.0, "GSM8741285 r1", "0:75", "A:441711745;C:218346228;G:242350714;T:374666966;N:175172", 75, null, null, null, 441711745, 218346228, 242350714, 374666966, 175172, "SRX27375422", "SRS23810886", "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"], [29137, "SRR32025068", "SRX27375421", "SRS23810885", "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, "smad3ab DKO 3 biol rep 1 5 dpf 5 fish pooled", "GSM8741284", null, "source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad3a/b DKO|geo loc name:missing|collection date:missing", "smad3ab DKO 3 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:smad3a/b DKO", "GSM8741284", "GSM8741284: smad3ab DKO 3 biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq", "GSM8741284 r1", "GSM8741284", "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, "18_smad3a__smad3b__B10_R1.fastq.gz", "fastq", 1564334850.0, 20857798.0, "GSM8741284 r1", "0:75", "A:538189348;C:271673806;G:298029553;T:456167924;N:274219", 75, null, null, null, 538189348, 271673806, 298029553, 456167924, 274219, "SRX27375421", "SRS23810885", "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"], [29138, "SRR32025069", "SRX27375420", "SRS23810883", "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, "smad3ab DKO 2 biol rep 1 5 dpf 5 fish pooled", "GSM8741283", null, "source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad3a/b DKO|geo loc name:missing|collection date:missing", "smad3ab DKO 2 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:smad3a/b DKO", "GSM8741283", "GSM8741283: smad3ab DKO 2 biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq", "GSM8741283 r1", "GSM8741283", "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, "17_smad3a__smad3b__A10_R1.fastq.gz", "fastq", 1496334900.0, 19951132.0, "GSM8741283 r1", "0:75", "A:514961004;C:254586630;G:285562274;T:440963052;N:261940", 75, null, null, null, 514961004, 254586630, 285562274, 440963052, 261940, "SRX27375420", "SRS23810883", "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"], [29139, "SRR32025070", "SRX27375419", "SRS23810884", "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, "smad3ab DKO 1 biol rep 1 5 dpf 5 fish pooled", "GSM8741282", null, "source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:smad3a/b DKO|geo loc name:missing|collection date:missing", "smad3ab DKO 1 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:smad3a/b DKO", "GSM8741282", "GSM8741282: smad3ab DKO 1 biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq", "GSM8741282 r1", "GSM8741282", "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, "16_smad3a__smad3b__H9_R1.fastq.gz", "fastq", 1403963250.0, 18719510.0, "GSM8741282 r1", "0:75", "A:488946191;C:233615962;G:269240931;T:411958629;N:201537", 75, null, null, null, 488946191, 233615962, 269240931, 411958629, 201537, "SRX27375419", "SRS23810884", "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"], [29140, "SRR32025071", "SRX27375418", "SRS23810882", "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 5 for smad3abDKO biol rep 1 5 dpf 5 fish pooled", "GSM8741281", 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 5 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", 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", "GSM8741281", "GSM8741281: control 5 for smad3abDKO biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq", "GSM8741281 r1", "GSM8741281", "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, "15_wt_control_G9_R1.fastq.gz", "fastq", 1565513400.0, 20873512.0, "GSM8741281 r1", "0:75", "A:537915091;C:264328012;G:304123957;T:458903666;N:242674", 75, null, null, null, 537915091, 264328012, 304123957, 458903666, 242674, "SRX27375418", "SRS23810882", "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"], [29141, "SRR32025072", "SRX27375417", "SRS23810881", "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 4 for smad3abDKO biol rep 1 5 dpf 5 fish pooled", "GSM8741280", 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 4 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", 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", "GSM8741280", "GSM8741280: control 4 for smad3abDKO biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq", "GSM8741280 r1", "GSM8741280", "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, "14_wt_control_F9_R1.fastq.gz", "fastq", 1289377350.0, 17191698.0, "GSM8741280 r1", "0:75", "A:444884871;C:212056955;G:249450087;T:382793805;N:191632", 75, null, null, null, 444884871, 212056955, 249450087, 382793805, 191632, "SRX27375417", "SRS23810881", "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"], [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\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 3 for smad3abDKO biol rep 1 5 dpf 5 fish pooled", "GSM8741279", 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 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", 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", "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\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, "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, null, null, null, 516842151, 249094684, 289026249, 444994403, 192213, "SRX27375416", "SRS23810880", "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"], [29143, "SRR32025074", "SRX27375415", "SRS23810879", "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 smad3abDKO biol rep 1 5 dpf 5 fish pooled", "GSM8741278", 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 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", 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", "GSM8741278", "GSM8741278: control 2 for smad3abDKO biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq", "GSM8741278 r1", "GSM8741278", "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, "12_wt_control_D9_R1.fastq.gz", "fastq", 1826731050.0, 24356414.0, "GSM8741278 r1", "0:75", "A:624589544;C:306590828;G:354308807;T:540924959;N:316912", 75, null, null, null, 624589544, 306590828, 354308807, 540924959, 316912, "SRX27375415", "SRS23810879", "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"], [29144, "SRR32025075", "SRX27375414", "SRS23810878", "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 1 for smad3abDKO biol rep 1 5 dpf 5 fish pooled", "GSM8741277", 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 1 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", 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", "GSM8741277", "GSM8741277: control 1 for smad3abDKO biol rep 1 5 dpf 5 fish pooled; Danio rerio; RNA Seq", "GSM8741277 r1", "GSM8741277", "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, "11_wt_control_C9_R1.fastq.gz", "fastq", 1657528425.0, 22100379.0, "GSM8741277 r1", "0:75", "A:567762447;C:276623380;G:320467937;T:492394510;N:280151", 75, null, null, null, 567762447, 276623380, 320467937, 492394510, 280151, "SRX27375414", "SRS23810878", "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"], [29145, "SRR32025076", "SRX27375413", "SRS23810876", "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, "qKO 5 biol rep 1 adult aorta 3 aortas pooled", "GSM8741276", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 5 biol rep 1 adult aorta 3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741276", "GSM8741276: qKO 5 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq", "GSM8741276 r1", "GSM8741276", "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, "10_qKO_B9_R1.fastq.gz", "fastq", 1749103950.0, 23321386.0, "GSM8741276 r1", "0:75", "A:608737363;C:302455983;G:338119173;T:499492171;N:299260", 75, null, null, null, 608737363, 302455983, 338119173, 499492171, 299260, "SRX27375413", "SRS23810876", "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", "Heart", "Cardiovascular System"], [29146, "SRR32025077", "SRX27375412", "SRS23810877", "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, "qKO 4 biol rep 1 adult aorta 3 aortas pooled", "GSM8741275", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 4 biol rep 1 adult aorta 3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741275", "GSM8741275: qKO 4 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq", "GSM8741275 r1", "GSM8741275", "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, "9_qKO_A9_R1.fastq.gz", "fastq", 1391151150.0, 18548682.0, "GSM8741275 r1", "0:75", "A:493715157;C:235480005;G:265878909;T:395857913;N:219166", 75, null, null, null, 493715157, 235480005, 265878909, 395857913, 219166, "SRX27375412", "SRS23810877", "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", "Heart", "Cardiovascular System"], [29147, "SRR32025078", "SRX27375411", "SRS23810875", "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, "qKO 3 biol rep 1 adult aorta 3 aortas pooled", "GSM8741274", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 3 biol rep 1 adult aorta 3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741274", "GSM8741274: qKO 3 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq", "GSM8741274 r1", "GSM8741274", "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, "8_qKO_H8_R1.fastq.gz", "fastq", 1548693000.0, 20649240.0, "GSM8741274 r1", "0:75", "A:546086416;C:265907989;G:302995102;T:433434795;N:268698", 75, null, null, null, 546086416, 265907989, 302995102, 433434795, 268698, "SRX27375411", "SRS23810875", "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", "Heart", "Cardiovascular System"], [29148, "SRR32025079", "SRX27375410", "SRS23810873", "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, "qKO 2 biol rep 1 adult aorta 3 aortas pooled", "GSM8741273", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 2 biol rep 1 adult aorta 3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741273", "GSM8741273: qKO 2 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq", "GSM8741273 r1", "GSM8741273", "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, "7_qKO_G8_R1.fastq.gz", "fastq", 1420837575.0, 18944501.0, "GSM8741273 r1", "0:75", "A:505066296;C:237130175;G:277345211;T:401058536;N:237357", 75, null, null, null, 505066296, 237130175, 277345211, 401058536, 237357, "SRX27375410", "SRS23810873", "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", "Heart", "Cardiovascular System"], [29149, "SRR32025080", "SRX27375409", "SRS23810874", "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, "qKO 1 biol rep 1 adult aorta 3 aortas pooled", "GSM8741272", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 1 biol rep 1 adult aorta 3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741272", "GSM8741272: qKO 1 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq", "GSM8741272 r1", "GSM8741272", "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, "6_qKO_F8_R1.fastq.gz", "fastq", 1486031025.0, 19813747.0, "GSM8741272 r1", "0:75", "A:520876345;C:250796628;G:293184034;T:420907913;N:266105", 75, null, null, null, 520876345, 250796628, 293184034, 420907913, 266105, "SRX27375409", "SRS23810874", "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", "Heart", "Cardiovascular System"], [29150, "SRR32025081", "SRX27375408", "SRS23810872", "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 5 biol rep 1 adult aorta 3 aortas pooled", "GSM8741271", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 5 biol rep 1 adult aorta 3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741271", "GSM8741271: control 5 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq", "GSM8741271 r1", "GSM8741271", "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, "5_wt_control_E8_R1.fastq.gz", "fastq", 1415975175.0, 18879669.0, "GSM8741271 r1", "0:75", "A:499498659;C:237283969;G:278581269;T:400389063;N:222215", 75, null, null, null, 499498659, 237283969, 278581269, 400389063, 222215, "SRX27375408", "SRS23810872", "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", "Heart", "Cardiovascular System"], [29151, "SRR32025082", "SRX27375407", "SRS23810871", "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 4 biol rep 1 adult aorta 3 aortas pooled", "GSM8741270", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 4 biol rep 1 adult aorta 3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741270", "GSM8741270: control 4 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq", "GSM8741270 r1", "GSM8741270", "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, "4_wt_control_D8_R1.fastq.gz", "fastq", 1448565375.0, 19314205.0, "GSM8741270 r1", "0:75", "A:515361139;C:240035739;G:286658162;T:406262131;N:248204", 75, null, null, null, 515361139, 240035739, 286658162, 406262131, 248204, "SRX27375407", "SRS23810871", "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", "Heart", "Cardiovascular System"], [29152, "SRR32025083", "SRX27375406", "SRS23810870", "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 3 biol rep 1 adult aorta 3 aortas pooled", "GSM8741269", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 3 biol rep 1 adult aorta 3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741269", "GSM8741269: control 3 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq", "GSM8741269 r1", "GSM8741269", "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, "3_wt_control_C8_R1.fastq.gz", "fastq", 1171513275.0, 15620177.0, "GSM8741269 r1", "0:75", "A:417371801;C:198042286;G:227929434;T:328006138;N:163616", 75, null, null, null, 417371801, 198042286, 227929434, 328006138, 163616, "SRX27375406", "SRS23810870", "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", "Heart", "Cardiovascular System"], [29153, "SRR32025084", "SRX27375405", "SRS23810869", "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 biol rep 1 adult aorta 3 aortas pooled", "GSM8741268", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 2 biol rep 1 adult aorta 3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741268", "GSM8741268: control 2 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq", "GSM8741268 r1", "GSM8741268", "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, "2_wt_control_B8_R1.fastq.gz", "fastq", 1379973000.0, 18399640.0, "GSM8741268 r1", "0:75", "A:487735196;C:232122567;G:270442978;T:389464154;N:208105", 75, null, null, null, 487735196, 232122567, 270442978, 389464154, 208105, "SRX27375405", "SRS23810869", "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", "Heart", "Cardiovascular System"], [29154, "SRR32025085", "SRX27375404", "SRS23810868", "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 1 biol rep 1 adult aorta 3 aortas pooled", "GSM8741267", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 1 biol rep 1 adult aorta 3 aortas 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 adult aortas and bulbus arteriosus", 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 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741267", "GSM8741267: control 1 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq", "GSM8741267 r1", "GSM8741267", "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, "1_wt_control_A8_R1.fastq.gz", "fastq", 1068193125.0, 14242575.0, "GSM8741267 r1", "0:75", "A:379776425;C:179521683;G:209337737;T:299415096;N:142184", 75, null, null, null, 379776425, 179521683, 209337737, 299415096, 142184, "SRX27375404", "SRS23810868", "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", "Heart", "Cardiovascular System"], [34364, "SRR31695142", "SRX27056958", "SRS23518718", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep4", "GSM8678154", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep4", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA", "GSM8678154", "GSM8678154: RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep4; Danio rerio; RNA Seq", "GSM8678154 r1", "GSM8678154", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g1Syn_rep4_R1.fastq.gz T_pRfxCas13d_g1Syn_rep4_R2.fastq.gz", "fastq fastq", 1869396000.0, 12462640.0, "GSM8678154 r1", "0:75 1:75", "A:497545631;C:434254877;G:436435676;T:501090064;N:69752", 75, 75, null, null, 497545631, 434254877, 436435676, 501090064, 69752, "SRX27056958", "SRS23518718", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34365, "SRR31695143", "SRX27056957", "SRS23518717", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep3", "GSM8678153", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep3", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA", "GSM8678153", "GSM8678153: RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep3; Danio rerio; RNA Seq", "GSM8678153 r1", "GSM8678153", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g1Syn_rep3_R1.fastq.gz T_pRfxCas13d_g1Syn_rep3_R2.fastq.gz", "fastq fastq", 1939758450.0, 12931723.0, "GSM8678153 r1", "0:75 1:75", "A:510928336;C:455303431;G:458245636;T:515206838;N:74209", 75, 75, null, null, 510928336, 455303431, 458245636, 515206838, 74209, "SRX27056957", "SRS23518717", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34366, "SRR31695144", "SRX27056956", "SRS23518716", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep4", "GSM8678152", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep4", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA", "GSM8678152", "GSM8678152: RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep4; Danio rerio; RNA Seq", "GSM8678152 r1", "GSM8678152", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g3Syn_rep4_R1.fastq.gz T_pRfxCas13d_g3Syn_rep4_R2.fastq.gz", "fastq fastq", 1372458150.0, 9149721.0, "GSM8678152 r1", "0:75 1:75", "A:363668106;C:319963774;G:322725620;T:366049498;N:51152", 75, 75, null, null, 363668106, 319963774, 322725620, 366049498, 51152, "SRX27056956", "SRS23518716", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34367, "SRR31695145", "SRX27056955", "SRS23518715", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep3", "GSM8678151", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep3", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA", "GSM8678151", "GSM8678151: RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep3; Danio rerio; RNA Seq", "GSM8678151 r1", "GSM8678151", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g3Syn_rep3_R1.fastq.gz T_pRfxCas13d_g3Syn_rep3_R2.fastq.gz", "fastq fastq", 1716718500.0, 11444790.0, "GSM8678151 r1", "0:75 1:75", "A:454308432;C:401470287;G:402968652;T:457908108;N:63021", 75, 75, null, null, 454308432, 401470287, 402968652, 457908108, 63021, "SRX27056955", "SRS23518715", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34368, "SRR31695150", "SRX27056954", "SRS23518714", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d control rep6", "GSM8678150", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control|geo loc name:missing|collection date:missing", "RfxCas13d control rep6", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control", "GSM8678150", "GSM8678150: RfxCas13d control rep6; Danio rerio; RNA Seq", "GSM8678150 r1", "GSM8678150", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_rep6_R1.fastq.gz T_pRfxCas13d_rep6_R2.fastq.gz", "fastq fastq", 1820554200.0, 12137028.0, "GSM8678150 r1", "0:75 1:75", "A:480817156;C:426951021;G:428763810;T:483952927;N:69286", 75, 75, null, null, 480817156, 426951021, 428763810, 483952927, 69286, "SRX27056954", "SRS23518714", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34369, "SRR31695146", "SRX27056953", "SRS23518713", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep2", "GSM8678149", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep2", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA", "GSM8678149", "GSM8678149: RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep2; Danio rerio; RNA Seq", "GSM8678149 r1", "GSM8678149", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g1Syn_rep2_R1.fastq.gz T_pRfxCas13d_g1Syn_rep2_R2.fastq.gz", "fastq fastq", 1686506550.0, 11243377.0, "GSM8678149 r1", "0:75 1:75", "A:445306390;C:395515087;G:396951869;T:448671449;N:61755", 75, 75, null, null, 445306390, 395515087, 396951869, 448671449, 61755, "SRX27056953", "SRS23518713", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34370, "SRR31695147", "SRX27056952", "SRS23518712", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep1", "GSM8678148", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep1", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA", "GSM8678148", "GSM8678148: RfxCas13d + g1 Chemically Synthesized si:dkey 93m18.4 rep1; Danio rerio; RNA Seq", "GSM8678148 r1", "GSM8678148", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g1Syn_rep1_R1.fastq.gz T_pRfxCas13d_g1Syn_rep1_R2.fastq.gz", "fastq fastq", 2099239050.0, 13994927.0, "GSM8678148 r1", "0:75 1:75", "A:555464950;C:490168575;G:492715156;T:560811934;N:78435", 75, 75, null, null, 555464950, 490168575, 492715156, 560811934, 78435, "SRX27056952", "SRS23518712", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34371, "SRR31695148", "SRX27056951", "SRS23518711", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep2", "GSM8678147", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep2", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA", "GSM8678147", "GSM8678147: RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep2; Danio rerio; RNA Seq", "GSM8678147 r1", "GSM8678147", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g3Syn_rep2_R1.fastq.gz T_pRfxCas13d_g3Syn_rep2_R2.fastq.gz", "fastq fastq", 1855616550.0, 12370777.0, "GSM8678147 r1", "0:75 1:75", "A:490735862;C:434070234;G:436325424;T:494415408;N:69622", 75, 75, null, null, 490735862, 434070234, 436325424, 494415408, 69622, "SRX27056951", "SRS23518711", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34372, "SRR31695149", "SRX27056950", "SRS23518710", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep1", "GSM8678146", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep1", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown Chemically Synthesized gRNA", "GSM8678146", "GSM8678146: RfxCas13d + g3 Chemically Synthesized si:dkey 93m18.4 rep1; Danio rerio; RNA Seq", "GSM8678146 r1", "GSM8678146", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g3Syn_rep1_R1.fastq.gz T_pRfxCas13d_g3Syn_rep1_R2.fastq.gz", "fastq fastq", 2029890750.0, 13532605.0, "GSM8678146 r1", "0:75 1:75", "A:536398630;C:474872197;G:478734292;T:539809587;N:76044", 75, 75, null, null, 536398630, 474872197, 478734292, 539809587, 76044, "SRX27056950", "SRS23518710", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34373, "SRR31695155", "SRX27056949", "SRS23518709", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d control rep5", "GSM8678145", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control|geo loc name:missing|collection date:missing", "RfxCas13d control rep5", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control", "GSM8678145", "GSM8678145: RfxCas13d control rep5; Danio rerio; RNA Seq", "GSM8678145 r1", "GSM8678145", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_rep5_R1.fastq.gz T_pRfxCas13d_rep5_R2.fastq.gz", "fastq fastq", 1699800000.0, 11332000.0, "GSM8678145 r1", "0:75 1:75", "A:448834438;C:398037498;G:400242751;T:452619971;N:65342", 75, 75, null, null, 448834438, 398037498, 400242751, 452619971, 65342, "SRX27056949", "SRS23518709", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34374, "SRR31695151", "SRX27056948", "SRS23518708", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g3 IVTed si:dkey 93m18.4 rep3", "GSM8678144", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown IVTed gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g3 IVTed si:dkey 93m18.4 rep3", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown IVTed gRNA", "GSM8678144", "GSM8678144: RfxCas13d + g3 IVTed si:dkey 93m18.4 rep3; Danio rerio; RNA Seq", "GSM8678144 r1", "GSM8678144", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g3_rep3_R1.fastq.gz T_pRfxCas13d_g3_rep3_R2.fastq.gz", "fastq fastq", 1603289100.0, 10688594.0, "GSM8678144 r1", "0:75 1:75", "A:420349766;C:379529179;G:379756700;T:423592677;N:60778", 75, 75, null, null, 420349766, 379529179, 379756700, 423592677, 60778, "SRX27056948", "SRS23518708", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34375, "SRR31695154", "SRX27056947", "SRS23518706", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g3 IVTed si:dkey 93m18.4 rep2", "GSM8678143", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown IVTed gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g3 IVTed si:dkey 93m18.4 rep2", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown IVTed gRNA", "GSM8678143", "GSM8678143: RfxCas13d + g3 IVTed si:dkey 93m18.4 rep2; Danio rerio; RNA Seq", "GSM8678143 r1", "GSM8678143", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g3_rep2_R1.fastq.gz T_pRfxCas13d_g3_rep2_R2.fastq.gz", "fastq fastq", 1700840400.0, 11338936.0, "GSM8678143 r1", "0:75 1:75", "A:447219410;C:401375108;G:401866426;T:450317233;N:62223", 75, 75, null, null, 447219410, 401375108, 401866426, 450317233, 62223, "SRX27056947", "SRS23518706", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34376, "SRR31695152", "SRX27056946", "SRS23518707", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d control rep4", "GSM8678142", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control|geo loc name:missing|collection date:missing", "RfxCas13d control rep4", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control", "GSM8678142", "GSM8678142: RfxCas13d control rep4; Danio rerio; RNA Seq", "GSM8678142 r1", "GSM8678142", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_rep4_R1.fastq.gz T_pRfxCas13d_rep4_R2.fastq.gz", "fastq fastq", 1390819050.0, 9272127.0, "GSM8678142 r1", "0:75 1:75", "A:365774543;C:327280225;G:328329658;T:369385513;N:49111", 75, 75, null, null, 365774543, 327280225, 328329658, 369385513, 49111, "SRX27056946", "SRS23518707", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34377, "SRR31695153", "SRX27056945", "SRS23518705", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g3 IVTed si:dkey 93m18.4 rep1", "GSM8678141", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown IVTed gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g3 IVTed si:dkey 93m18.4 rep1", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown IVTed gRNA", "GSM8678141", "GSM8678141: RfxCas13d + g3 IVTed si:dkey 93m18.4 rep1; Danio rerio; RNA Seq", "GSM8678141 r1", "GSM8678141", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g3_rep1_R1.fastq.gz T_pRfxCas13d_g3_rep1_R2.fastq.gz", "fastq fastq", 1979083650.0, 13193891.0, "GSM8678141 r1", "0:75 1:75", "A:521444446;C:467332323;G:468450230;T:521779923;N:76728", 75, 75, null, null, 521444446, 467332323, 468450230, 521779923, 76728, "SRX27056945", "SRS23518705", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34378, "SRR31695156", "SRX27056944", "SRS23518704", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d control rep3", "GSM8678140", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control|geo loc name:missing|collection date:missing", "RfxCas13d control rep3", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control", "GSM8678140", "GSM8678140: RfxCas13d control rep3; Danio rerio; RNA Seq", "GSM8678140 r1", "GSM8678140", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_rep3_R1.fastq.gz T_pRfxCas13d_rep3_R2.fastq.gz", "fastq fastq", 1520356800.0, 10135712.0, "GSM8678140 r1", "0:75 1:75", "A:400447283;C:357034714;G:358393387;T:404426537;N:54879", 75, 75, null, null, 400447283, 357034714, 358393387, 404426537, 54879, "SRX27056944", "SRS23518704", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34379, "SRR31695157", "SRX27056943", "SRS23518703", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g1 IVTed si:dkey 93m18.4 rep3", "GSM8678139", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown IVTed gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g1 IVTed si:dkey 93m18.4 rep3", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown IVTed gRNA", "GSM8678139", "GSM8678139: RfxCas13d + g1 IVTed si:dkey 93m18.4 rep3; Danio rerio; RNA Seq", "GSM8678139 r1", "GSM8678139", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g1_rep3_R1.fastq.gz T_pRfxCas13d_g1_rep3_R2.fastq.gz", "fastq fastq", 1890203250.0, 12601355.0, "GSM8678139 r1", "0:75 1:75", "A:501821472;C:441868721;G:441485425;T:504956362;N:71270", 75, 75, null, null, 501821472, 441868721, 441485425, 504956362, 71270, "SRX27056943", "SRS23518703", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34380, "SRR31695162", "SRX27056942", "SRS23518702", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g2 IVTed si:dkey 93m18.4 rep3", "GSM8678138", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown IVTed gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g2 IVTed si:dkey 93m18.4 rep3", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown IVTed gRNA", "GSM8678138", "GSM8678138: RfxCas13d + g2 IVTed si:dkey 93m18.4 rep3; Danio rerio; RNA Seq", "GSM8678138 r1", "GSM8678138", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g2_rep3_R1.fastq.gz T_pRfxCas13d_g2_rep3_R2.fastq.gz", "fastq fastq", 1839509400.0, 12263396.0, "GSM8678138 r1", "0:75 1:75", "A:485779725;C:432231942;G:432933832;T:488492257;N:71644", 75, 75, null, null, 485779725, 432231942, 432933832, 488492257, 71644, "SRX27056942", "SRS23518702", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34381, "SRR31695158", "SRX27056941", "SRS23518701", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g1 IVTed si:dkey 93m18.4 rep2", "GSM8678137", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown IVTed gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g1 IVTed si:dkey 93m18.4 rep2", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown IVTed gRNA", "GSM8678137", "GSM8678137: RfxCas13d + g1 IVTed si:dkey 93m18.4 rep2; Danio rerio; RNA Seq", "GSM8678137 r1", "GSM8678137", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g1_rep2_R1.fastq.gz T_pRfxCas13d_g1_rep2_R2.fastq.gz", "fastq fastq", 1742339250.0, 11615595.0, "GSM8678137 r1", "0:75 1:75", "A:461346904;C:406656276;G:409937021;T:464333259;N:65790", 75, 75, null, null, 461346904, 406656276, 409937021, 464333259, 65790, "SRX27056941", "SRS23518701", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34382, "SRR31695161", "SRX27056940", "SRS23518700", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d control rep2", "GSM8678136", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control|geo loc name:missing|collection date:missing", "RfxCas13d control rep2", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control", "GSM8678136", "GSM8678136: RfxCas13d control rep2; Danio rerio; RNA Seq", "GSM8678136 r1", "GSM8678136", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_rep2_R1.fastq.gz T_pRfxCas13d_rep2_R2.fastq.gz", "fastq fastq", 1800739800.0, 12004932.0, "GSM8678136 r1", "0:75 1:75", "A:477337887;C:421087001;G:421493244;T:480753457;N:68211", 75, 75, null, null, 477337887, 421087001, 421493244, 480753457, 68211, "SRX27056940", "SRS23518700", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34383, "SRR31695159", "SRX27056939", "SRS23518699", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g2 IVTed si:dkey 93m18.4 rep2", "GSM8678135", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown IVTed gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g2 IVTed si:dkey 93m18.4 rep2", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown IVTed gRNA", "GSM8678135", "GSM8678135: RfxCas13d + g2 IVTed si:dkey 93m18.4 rep2; Danio rerio; RNA Seq", "GSM8678135 r1", "GSM8678135", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g2_rep2_R1.fastq.gz T_pRfxCas13d_g2_rep2_R2.fastq.gz", "fastq fastq", 1752030300.0, 11680202.0, "GSM8678135 r1", "0:75 1:75", "A:462116558;C:411708555;G:412346341;T:465792629;N:66217", 75, 75, null, null, 462116558, 411708555, 412346341, 465792629, 66217, "SRX27056939", "SRS23518699", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34384, "SRR31695160", "SRX27056938", "SRS23518698", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g1 IVTed si:dkey 93m18.4 rep1", "GSM8678134", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown IVTed gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g1 IVTed si:dkey 93m18.4 rep1", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown IVTed gRNA", "GSM8678134", "GSM8678134: RfxCas13d + g1 IVTed si:dkey 93m18.4 rep1; Danio rerio; RNA Seq", "GSM8678134 r1", "GSM8678134", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g1_rep1_R1.fastq.gz T_pRfxCas13d_g1_rep1_R2.fastq.gz", "fastq fastq", 1724105250.0, 11494035.0, "GSM8678134 r1", "0:75 1:75", "A:456793309;C:403294318;G:403256373;T:460696014;N:65236", 75, 75, null, null, 456793309, 403294318, 403256373, 460696014, 65236, "SRX27056938", "SRS23518698", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34385, "SRR31695163", "SRX27056937", "SRS23518697", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d + g2 IVTed si:dkey 93m18.4 rep1", "GSM8678133", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:Knockdown IVTed gRNA|geo loc name:missing|collection date:missing", "RfxCas13d + g2 IVTed si:dkey 93m18.4 rep1", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:Knockdown IVTed gRNA", "GSM8678133", "GSM8678133: RfxCas13d + g2 IVTed si:dkey 93m18.4 rep1; Danio rerio; RNA Seq", "GSM8678133 r1", "GSM8678133", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ELEMENT", "Element AVITI", null, "SRP551059", null, null, "T_pRfxCas13d_g2_rep1_R1.fastq.gz T_pRfxCas13d_g2_rep1_R2.fastq.gz", "fastq fastq", 1903402350.0, 12689349.0, "GSM8678133 r1", "0:75 1:75", "A:501904806;C:447043548;G:448270395;T:506113883;N:69718", 75, 75, null, null, 501904806, 447043548, 448270395, 506113883, 69718, "SRX27056937", "SRS23518697", "SRA2032641", "Stowers Institute for Medical Research", "Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "element", "element", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-12-12", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [34386, "SRR31695164", "SRX27056936", "SRS23518696", "SRP551059", "PRJNA1197382", "Enhanced RNA targeting CRISPR Cas technology in zebrafish V", "GSE284120", "Transcriptome Analysis", "Transient elimination of RNAs by CRISPR Cas13 systems has been widely used in basic and applied sciences over the last years. However the efficiency of the system can be enhanced in vivo and its application has generated controversy due to the recently described collateral activity in mammalian cells and mouse models. Here we have optimized the CRISPR RfxCas13d CasRx system for an optimized RNA targeting in vivo in zebrafish embryos by different and compatible approaches. These strategies include the use of chemically modified guide RNAs to increase and sustain mRNA knockdown an improved nuclear targeting and the evaluation of ex vivo computational models for predicting gRNA efficiency in vivo. Furthermore our study demonstrated that transient CRISPR RfxCas13d approaches can effectively deplete endogenous mRNAs in zebrafish embryos without xxx collateral effects except for targeting extremely abundant RNAs. For that we have implemented alternative RNA targeting CRISPR Cas systems with reduced or absent collateral activity in zebrafish embryos. Altogether these findings contribute to optimize CRISPR Cas technology for RNA targeting in zebrafish through transient approaches and assist the progress of potential implications for knockdown therapies in vivo. Overall design: To investigate the toxicity effect of IVTed gRNAs compared with chemically synthesized", "parent bioproject:PRJNA1128082", "pubmed:40091120", null, "RfxCas13d control rep1", "GSM8678132", null, "source name:whole embryo|tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control|geo loc name:missing|collection date:missing", "RfxCas13d control rep1", "Following sequencing Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files. Assembly: danrer11 Supplementary files format and content: tab delimited txt file includes raw counts for each Sample", "whole embryo", null, "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer\u2019s instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. Equal molar libraries were pooled quantified and converted to process on the Element AVITI.", null, "tissue:whole embryo|age:4 hpf|treatment:RfxCas13d control", "GSM8678132", "GSM8678132: RfxCas13d control rep1; Danio rerio; RNA Seq", "GSM8678132 r1", "GSM8678132", "1", "Total RNA then was extracted using Direct zol RNA Miniprep Kit #R2050 Zymo Research following manufacturer's instructions. Zebrafish embryos total RNA sequencing libraries were generated from 100 ng of high quality total RNA as assessed using the Bioanalyzer Agilent with the Watchmaker mRNA Library Prep Kit Watchmaker Cat. No. 7BK0001 at a 1/5th reaction volume. mRNA isolation and library construction were completed per protocol at the miniaturization scale. For Library amplification 2 \u00b5L of IDT indexed primers using xGen\u2122 Stubby Adapter UDI Primers 96 reactions Cat No. 10005921 was added to 3 \u00b5L of library and 5 \u00b5L of Equinox Amplification Master Mix 2x. These libraries were then amplified for 12 cycles of PCR using an annealing temperature of 55\u00b0C according to step 10.2. 1.0x SPRISelect Beckman Coulter Cat. No. B23318 bead ratio was used during the Post Amplification Cleanup and post amplification libraries were eluted in 10 \u00b5L of Qiagen EB Qiagen Cat. No. 19086. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer and the Qubit Flex Fluorometer Life Technologies. 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"devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"experiment.platform\" = :p0 order by rowid limit 101", "params": {"p0": "ELEMENT"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.platform=ELEMENT", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 53, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ELEMENT&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.platform=ELEMENT", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 53, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ELEMENT&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.platform=ELEMENT", "results": [{"value": "cDNA", "label": "cDNA", "count": 53, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ELEMENT&experiment.library_selection=cDNA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.platform=ELEMENT", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ELEMENT&experiment.library_layout=SINGLE", "selected": false}, {"value": "PAIRED", "label": "PAIRED", "count": 23, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ELEMENT&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.platform=ELEMENT", "results": [{"value": "ELEMENT", "label": "ELEMENT", "count": 53, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json", "selected": true}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.platform=ELEMENT", "results": [{"value": "Multi-stage", "label": "Multi-stage", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ELEMENT&devstage_curation_coarse=Multi-stage", "selected": false}, {"value": "Embryo", "label": "Embryo", "count": 23, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ELEMENT&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.platform=ELEMENT", "results": [{"value": "Multi-stage", "label": "Multi-stage", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ELEMENT&devstage_curation=Multi-stage", "selected": false}, {"value": "Blastula", "label": "Blastula", "count": 23, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ELEMENT&devstage_curation=Blastula", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.platform=ELEMENT", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 43, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ELEMENT&tissue_curation_coarse=All+anatomical+structures", "selected": false}, {"value": "Cardiovascular System", "label": "Cardiovascular System", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ELEMENT&tissue_curation_coarse=Cardiovascular+System", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.platform=ELEMENT", "results": [{"value": "Whole Organism", "label": "Whole Organism", "count": 43, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ELEMENT&tissue_curation=Whole+Organism", "selected": false}, {"value": "Heart", "label": "Heart", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ELEMENT&tissue_curation=Heart", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.platform=ELEMENT", "results": [{"value": "unknown", "label": "unknown", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ELEMENT&technology=unknown", "selected": false}, {"value": "bulk", "label": "bulk", "count": 23, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ELEMENT&technology=bulk", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 77.15342099982081}