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
9825,ERR2102841,ERX2160152,ERS1883528,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N3 nabu RNA,SAMEA104224510,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224510|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N3 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N3 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N3 nabu RNA s,N3 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N3_R1_all.fastq.gz,fastq,1410139550.0,18670564.0,E MTAB 5992:N3 nabu RNA,0:75.53 1:0,A:353294009;C:340727934;G:322476371;T:393200193;N:441043,75,0,,,353294009,340727934,322476371,393200193,441043,ERX2160152,ERS1883528,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95434,,0.08906,,0.66935,,0.47788,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9826,ERR2102840,ERX2160151,ERS1883527,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N2 nabu RNA,SAMEA104224509,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224509|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N2 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N2 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N2 nabu RNA s,N2 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N2_R1_all.fastq.gz,fastq,1478621168.0,19576865.0,E MTAB 5992:N2 nabu RNA,0:75.53 1:0,A:369453299;C:359092235;G:341176884;T:408389810;N:508940,75,0,,,369453299,359092235,341176884,408389810,508940,ERX2160151,ERS1883527,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95582,,0.08202,,0.67718,,0.47812,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9827,ERR2102839,ERX2160150,ERS1883526,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N1 nabu RNA,SAMEA104224508,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224508|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N1 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N1 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N1 nabu RNA s,N1 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N1_R1_all.fastq.gz,fastq,1531713181.0,20277882.0,E MTAB 5992:N1 nabu RNA,0:75.54 1:0,A:386600603;C:373317031;G:350339456;T:420938891;N:517200,75,0,,,386600603,373317031,350339456,420938891,517200,ERX2160150,ERS1883526,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.9552,,0.08124,,0.67685,,0.47578,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9828,ERR2102838,ERX2160149,ERS1883525,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C3 control RNA,SAMEA104224507,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224507|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C3 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C3 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C3 control RNA s,C3 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C3_R1_all.fastq.gz,fastq,1380662008.0,18279108.0,E MTAB 5992:C3 control RNA,0:75.53 1:0,A:345997031;C:338444594;G:316575258;T:379195977;N:449148,75,0,,,345997031,338444594,316575258,379195977,449148,ERX2160149,ERS1883525,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95615,,0.08131,,0.68694,,0.45267,,74,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9829,ERR2102837,ERX2160148,ERS1883524,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C2 control RNA,SAMEA104224506,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224506|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C2 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C2 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C2 control RNA s,C2 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C2_R1_all.fastq.gz,fastq,1336640735.0,17695627.0,E MTAB 5992:C2 control RNA,0:75.54 1:0,A:338213530;C:326808990;G:303983789;T:367147896;N:486530,75,0,,,338213530,326808990,303983789,367147896,486530,ERX2160148,ERS1883524,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95427,,0.08628,,0.67706,,0.47245,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9830,ERR2102836,ERX2160147,ERS1883523,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C1 control RNA,SAMEA104224505,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224505|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C1 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C1 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C1 control RNA s,C1 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C1_R1_all.fastq.gz,fastq,1297694845.0,17180544.0,E MTAB 5992:C1 control RNA,0:75.53 1:0,A:322048172;C:316542683;G:299227724;T:359449433;N:426833,75,0,,,322048172,316542683,299227724,359449433,426833,ERX2160147,ERS1883523,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95505,,0.08541,,0.67659,,0.48159,,75,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10141,ERR4973564,ERX4792138,ERS5459722,ERP125703,PRJEB41864,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9899,Transcriptome Analysis,mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced.,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,sibling 3,SAMEA7703213,Centre for Developmental Neurobiology King's College London,ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703213|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sibling 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 9899:sibling 3,,,,,,,,,NextSeq 500 sequencing; 3 prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9899:sibling 3 s,sibling 3 s,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RACE,SINGLE,ILLUMINA,NextSeq 500,,ERP125703,NextSeq 500 sequencing; three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,70_AACCGA_70_ACTAGC_S2_R1_001.fastq.gz,fastq,,,E MTAB 9899:sibling 3,0:76 1:0,A:385382600;C:210104151;G:238678838;T:315495923;N:5536,76,0,,,385382600,210104151,238678838,315495923,5536,ERX4792138,ERS5459722,ERA3194022,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,1,0.82613,,0.13111,,0.77597,,0.53833,,76,,B,,usable mapping rate,illumina,nextseq,3prime,other,lexogen,bulk,unknown,unknown,,United Kingdom,2020-12-10,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10142,ERR4973563,ERX4792137,ERS5459721,ERP125703,PRJEB41864,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9899,Transcriptome Analysis,mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced.,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,sibling 2,SAMEA7703212,Centre for Developmental Neurobiology King's College London,ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703212|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sibling 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 9899:sibling 2,,,,,,,,,NextSeq 500 sequencing; 3 prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9899:sibling 2 s,sibling 2 s,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RACE,SINGLE,ILLUMINA,NextSeq 500,,ERP125703,NextSeq 500 sequencing; three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,69_AGTTGA_69_CTTACA_S7_R1_001.fastq.gz,fastq,,,E MTAB 9899:sibling 2,0:76 1:0,A:405337161;C:226099266;G:255734601;T:341120121;N:5955,76,0,,,405337161,226099266,255734601,341120121,5955,ERX4792137,ERS5459721,ERA3194022,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,1,0.84066,,0.12241,,0.77755,,0.56472,,76,,B,,usable mapping rate,illumina,nextseq,3prime,other,lexogen,bulk,unknown,unknown,,United Kingdom,2020-12-10,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10143,ERR4973562,ERX4792136,ERS5459720,ERP125703,PRJEB41864,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9899,Transcriptome Analysis,mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced.,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,sibling 1,SAMEA7703211,Centre for Developmental Neurobiology King's College London,ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703211|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sibling 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 9899:sibling 1,,,,,,,,,NextSeq 500 sequencing; 3 prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9899:sibling 1 s,sibling 1 s,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,RACE,SINGLE,ILLUMINA,NextSeq 500,,ERP125703,NextSeq 500 sequencing; three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,68_CCAATT_68_GTCCCG_S11_R1_001.fastq.gz,fastq,,,E MTAB 9899:sibling 1,0:76 1:0,A:440539801;C:236835299;G:268057277;T:355636994;N:6169,76,0,,,440539801,236835299,268057277,355636994,6169,ERX4792136,ERS5459720,ERA3194022,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,1,0.82002,,0.12908,,0.77766,,0.54981,,76,,B,,usable mapping rate,illumina,nextseq,3prime,other,lexogen,bulk,unknown,unknown,,United Kingdom,2020-12-10,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10144,ERR4973561,ERX4792135,ERS5459719,ERP125703,PRJEB41864,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9899,Transcriptome Analysis,mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced.,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,sfpq 3,SAMEA7703210,Centre for Developmental Neurobiology King's College London,ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703210|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sfpq 3|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:sfpq / |organism part:whole organism|sample name:E MTAB 9899:sfpq 3,,,,,,,,,NextSeq 500 sequencing; 3 prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9899:sfpq 3 s,sfpq 3 s,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,Experimental Factor: genotype:sfpq / ,RNA-Seq,TRANSCRIPTOMIC,RACE,SINGLE,ILLUMINA,NextSeq 500,,ERP125703,NextSeq 500 sequencing; three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,67_TCGTTC_67_TGCTAT_S22_R1_001.fastq.gz,fastq,,,E MTAB 9899:sfpq 3,0:76 1:0,A:493165327;C:268347233;G:303443918;T:399152596;N:7138,76,0,,,493165327,268347233,303443918,399152596,7138,ERX4792135,ERS5459719,ERA3194022,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,1,0.82521,,0.12349,,0.78545,,0.57446,,76,,B,,usable mapping rate,illumina,nextseq,3prime,other,lexogen,bulk,unknown,unknown,,United Kingdom,2020-12-10,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10145,ERR4973560,ERX4792134,ERS5459718,ERP125703,PRJEB41864,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9899,Transcriptome Analysis,mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced.,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,sfpq 2,SAMEA7703209,Centre for Developmental Neurobiology King's College London,ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703209|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sfpq 2|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:sfpq / |organism part:whole organism|sample name:E MTAB 9899:sfpq 2,,,,,,,,,NextSeq 500 sequencing; 3 prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9899:sfpq 2 s,sfpq 2 s,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,Experimental Factor: genotype:sfpq / ,RNA-Seq,TRANSCRIPTOMIC,RACE,SINGLE,ILLUMINA,NextSeq 500,,ERP125703,NextSeq 500 sequencing; three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,66_GACGAT_66_TCAGTC_S18_R1_001.fastq.gz,fastq,,,E MTAB 9899:sfpq 2,0:76 1:0,A:426637005;C:227027693;G:257342561;T:338159540;N:5909,76,0,,,426637005,227027693,257342561,338159540,5909,ERX4792134,ERS5459718,ERA3194022,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,1,0.81933,,0.11571,,0.78593,,0.56675,,76,,B,,usable mapping rate,illumina,nextseq,3prime,other,lexogen,bulk,unknown,unknown,,United Kingdom,2020-12-10,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
10146,ERR4973559,ERX4792133,ERS5459717,ERP125703,PRJEB41864,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E-MTAB-9899,Transcriptome Analysis,mRNA was purified from whole zebrafish embryos at 24 hpf and three prime proximal region was sequenced.,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,,Protocols: Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,sfpq 1,SAMEA7703208,Centre for Developmental Neurobiology King's College London,ENA first public:2021 01 27|ENA last update:2020 12 10|External Id:SAMEA7703208|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2021 01 27T17:06:57Z|INSDC last update:2020 12 10T17:23:32Z|INSDC status:public|Submitter Id:E MTAB 9899:sfpq 1|age:24|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:sfpq / |organism part:whole organism|sample name:E MTAB 9899:sfpq 1,,,,,,,,,NextSeq 500 sequencing; 3 prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,E MTAB 9899:sfpq 1 s,sfpq 1 s,three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,Embryos were collected from in crosses of sfpq+/  adult zebrafish RNA was extracted using the RNEasy Mini Kit Qiagen Library was generated using Lexogen's QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina,Experimental Factor: genotype:sfpq / ,RNA-Seq,TRANSCRIPTOMIC,RACE,SINGLE,ILLUMINA,NextSeq 500,,ERP125703,NextSeq 500 sequencing; three prime mRNA seq of sfpq /  zebrafish embryos and siblings at 24 hpf,ENA FIRST PUBLIC:2021 01 27|ENA LAST UPDATE:2020 12 10,65_AAGCTC_65_AAGAAG_S3_R1_001.fastq.gz,fastq,,,E MTAB 9899:sfpq 1,0:76 1:0,A:425613638;C:225707961;G:254738302;T:336863560;N:5847,76,0,,,425613638,225707961,254738302,336863560,5847,ERX4792133,ERS5459717,ERA3194022,Centre for Developmental Neurobiology King,Centre for Developmental Neurobiology King,1,0.81857,,0.11342,,0.78587,,0.56439,,76,,B,,usable mapping rate,illumina,nextseq,3prime,other,lexogen,bulk,unknown,unknown,,United Kingdom,2020-12-10,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® 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.,,,,smad6ab DKO 5  biol rep 1  5 dpf  5 fish pooled,GSM8741296,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype: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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,612499747,307171870,341630182,521913046,316805,SRX27375433,SRS23810897,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® 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.,,,,smad6ab DKO 4  biol rep 1  5 dpf  5 fish pooled,GSM8741295,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype: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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,610799963,310255661,349091544,536431072,317485,SRX27375432,SRS23810896,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® 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.,,,,smad6ab DKO 3  biol rep 1  5 dpf  5 fish pooled,GSM8741294,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype: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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,417424019,209354549,238058828,371172361,152618,SRX27375431,SRS23810895,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® 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.,,,,smad6ab DKO 2  biol rep 1  5 dpf  5 fish pooled,GSM8741293,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype: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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,422806413,210247744,238495376,367964420,207097,SRX27375430,SRS23810893,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® 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.,,,,smad6ab DKO 1  biol rep 1  5 dpf  5 fish pooled,GSM8741292,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype: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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,600616051,303681611,340472236,526419468,309434,SRX27375429,SRS23810894,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 5 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741291,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,544358067,268587913,299883067,461155939,270039,SRX27375428,SRS23810892,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 4 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741290,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,413692477,202818991,227848971,353083087,170274,SRX27375427,SRS23810891,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 3 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741289,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,493379384,244908245,274361129,420258548,247444,SRX27375426,SRS23810890,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 2 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741288,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,442456808,219464610,244269392,377385874,219166,SRX27375425,SRS23810888,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 1 for smad6abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741287,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,556979571,275622807,309210789,478725788,248545,SRX27375424,SRS23810889,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® 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.,,,,smad3ab DKO 5  biol rep 1  5 dpf  5 fish pooled,GSM8741286,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype: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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,575504153,284148304,316755855,487400701,258887,SRX27375423,SRS23810887,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® 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.,,,,smad3ab DKO 4  biol rep 1  5 dpf  5 fish pooled,GSM8741285,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype: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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,441711745,218346228,242350714,374666966,175172,SRX27375422,SRS23810886,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® 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.,,,,smad3ab DKO 3  biol rep 1  5 dpf  5 fish pooled,GSM8741284,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype: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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,538189348,271673806,298029553,456167924,274219,SRX27375421,SRS23810885,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® 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.,,,,smad3ab DKO 2  biol rep 1  5 dpf  5 fish pooled,GSM8741283,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype: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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,514961004,254586630,285562274,440963052,261940,SRX27375420,SRS23810883,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® 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.,,,,smad3ab DKO 1  biol rep 1  5 dpf  5 fish pooled,GSM8741282,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype: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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,488946191,233615962,269240931,411958629,201537,SRX27375419,SRS23810884,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 5 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741281,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,537915091,264328012,304123957,458903666,242674,SRX27375418,SRS23810882,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 4 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741280,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,444884871,212056955,249450087,382793805,191632,SRX27375417,SRS23810881,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29142,SRR32025073,SRX27375416,SRS23810880,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 3 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741279,,source name:pool of 3 whole embryos|tissue:pool of 3 whole embryos|genotype:wt control|geo loc name:missing|collection date:missing,control 3 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 whole embryos,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,GSM8741279,GSM8741279: control 3 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled; Danio rerio; RNA Seq,GSM8741279 r1,GSM8741279,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,13_wt_control_E9_R1.fastq.gz,fastq,1500149700.0,20001996.0,GSM8741279 r1,0:75,A:516842151;C:249094684;G:289026249;T:444994403;N:192213,75,,,,516842151,249094684,289026249,444994403,192213,SRX27375416,SRS23810880,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 2 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741278,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,624589544,306590828,354308807,540924959,316912,SRX27375415,SRS23810879,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 1 for smad3abDKO  biol rep 1  5 dpf  5 fish pooled,GSM8741277,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 whole embryos|genotype:wt control,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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,567762447,276623380,320467937,492394510,280151,SRX27375414,SRS23810878,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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® 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.,,,,qKO 5  biol rep 1  adult aorta  3 aortas pooled,GSM8741276,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,608737363,302455983,338119173,499492171,299260,SRX27375413,SRS23810876,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,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® 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.,,,,qKO 4  biol rep 1  adult aorta  3 aortas pooled,GSM8741275,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,493715157,235480005,265878909,395857913,219166,SRX27375412,SRS23810877,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,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® 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.,,,,qKO 3  biol rep 1  adult aorta  3 aortas pooled,GSM8741274,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,546086416,265907989,302995102,433434795,268698,SRX27375411,SRS23810875,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,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® 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.,,,,qKO 2  biol rep 1  adult aorta  3 aortas pooled,GSM8741273,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,505066296,237130175,277345211,401058536,237357,SRX27375410,SRS23810873,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,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® 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.,,,,qKO 1  biol rep 1  adult aorta  3 aortas pooled,GSM8741272,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,520876345,250796628,293184034,420907913,266105,SRX27375409,SRS23810874,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 5  biol rep 1  adult aorta  3 aortas pooled,GSM8741271,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,499498659,237283969,278581269,400389063,222215,SRX27375408,SRS23810872,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 4  biol rep 1  adult aorta  3 aortas pooled,GSM8741270,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,515361139,240035739,286658162,406262131,248204,SRX27375407,SRS23810871,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 3  biol rep 1  adult aorta  3 aortas pooled,GSM8741269,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,417371801,198042286,227929434,328006138,163616,SRX27375406,SRS23810870,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 2  biol rep 1  adult aorta  3 aortas pooled,GSM8741268,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,487735196,232122567,270442978,389464154,208105,SRX27375405,SRS23810869,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 1  biol rep 1  adult aorta  3 aortas pooled,GSM8741267,,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,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 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® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,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,,,,379776425,179521683,209337737,299415096,142184,SRX27375404,SRS23810868,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Heart,Cardiovascular System
29677,SRR27406946,SRX23082021,SRS20040790,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 6 s   2 [IL 13 30 32],GSM8001105,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:6 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 6 s   2 [IL 13 30 32],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:6 dpf|tissue:whole embryo/larva,GSM8001105,GSM8001105: m 6 s   2 [IL 13 30 32]; Danio rerio; RNA Seq,GSM8001105 r1,GSM8001105,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-32_CGTACG_L001_R1_001.fastq.gz,fastq,416057592.0,8157992.0,GSM8001105 r1,0:51,A:102142103;C:101373914;G:97024244;T:115471134;N:46197,51,,,,102142103,101373914,97024244,115471134,46197,SRX23082021,SRS20040790,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29678,SRR27406947,SRX23082021,SRS20040790,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 6 s   2 [IL 13 30 32],GSM8001105,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:6 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 6 s   2 [IL 13 30 32],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:6 dpf|tissue:whole embryo/larva,GSM8001105,GSM8001105: m 6 s   2 [IL 13 30 32]; Danio rerio; RNA Seq,GSM8001105 r1,GSM8001105,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-32_CGTACG_L002_R1_001.fastq.gz,fastq,424539249.0,8324299.0,GSM8001105 r2,0:51,A:104318858;C:103391735;G:98951259;T:117859918;N:17479,51,,,,104318858,103391735,98951259,117859918,17479,SRX23082021,SRS20040790,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29679,SRR27406948,SRX23082020,SRS20040788,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 6 s [IL 13 30 31],GSM8001104,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:6 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 6 s [IL 13 30 31],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:6 dpf|tissue:whole embryo/larva,GSM8001104,GSM8001104: p 6 s [IL 13 30 31]; Danio rerio; RNA Seq,GSM8001104 r1,GSM8001104,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-31_GTTTCG_L001_R1_001.fastq.gz,fastq,336956082.0,6606982.0,GSM8001104 r1,0:51,A:81805829;C:82575847;G:78870721;T:93667461;N:36224,51,,,,81805829,82575847,78870721,93667461,36224,SRX23082020,SRS20040788,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29680,SRR27406949,SRX23082020,SRS20040788,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 6 s [IL 13 30 31],GSM8001104,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:6 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 6 s [IL 13 30 31],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:6 dpf|tissue:whole embryo/larva,GSM8001104,GSM8001104: p 6 s [IL 13 30 31]; Danio rerio; RNA Seq,GSM8001104 r1,GSM8001104,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-31_GTTTCG_L002_R1_001.fastq.gz,fastq,343735920.0,6739920.0,GSM8001104 r2,0:51,A:83495446;C:84252532;G:80385387;T:95588863;N:13692,51,,,,83495446,84252532,80385387,95588863,13692,SRX23082020,SRS20040788,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29681,SRR27406950,SRX23082019,SRS20040789,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 4 s [IL 13 30 30],GSM8001103,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 4 s [IL 13 30 30],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva,GSM8001103,GSM8001103: m 4 s [IL 13 30 30]; Danio rerio; RNA Seq,GSM8001103 r1,GSM8001103,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-30_GTGGCC_L001_R1_001.fastq.gz,fastq,325837674.0,6388974.0,GSM8001103 r1,0:51,A:80805848;C:78380749;G:75147290;T:91467315;N:36472,51,,,,80805848,78380749,75147290,91467315,36472,SRX23082019,SRS20040789,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29682,SRR27406951,SRX23082019,SRS20040789,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 4 s [IL 13 30 30],GSM8001103,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 4 s [IL 13 30 30],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva,GSM8001103,GSM8001103: m 4 s [IL 13 30 30]; Danio rerio; RNA Seq,GSM8001103 r1,GSM8001103,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-30_GTGGCC_L002_R1_001.fastq.gz,fastq,333111549.0,6531599.0,GSM8001103 r2,0:51,A:82692565;C:80092634;G:76757552;T:93555769;N:13029,51,,,,82692565,80092634,76757552,93555769,13029,SRX23082019,SRS20040789,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29683,SRR27406952,SRX23082018,SRS20040786,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 4 2 [IL 13 30 29],GSM8001102,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 4 2 [IL 13 30 29],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva,GSM8001102,GSM8001102: m 4 2 [IL 13 30 29]; Danio rerio; RNA Seq,GSM8001102 r1,GSM8001102,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-29_GGCTAC_L001_R1_001.fastq.gz,fastq,197899227.0,3880377.0,GSM8001102 r1,0:51,A:48874076;C:47852911;G:45809628;T:55339675;N:22937,51,,,,48874076,47852911,45809628,55339675,22937,SRX23082018,SRS20040786,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29684,SRR27406953,SRX23082018,SRS20040786,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 4 2 [IL 13 30 29],GSM8001102,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 4 2 [IL 13 30 29],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva,GSM8001102,GSM8001102: m 4 2 [IL 13 30 29]; Danio rerio; RNA Seq,GSM8001102 r1,GSM8001102,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-29_GGCTAC_L002_R1_001.fastq.gz,fastq,201408027.0,3949177.0,GSM8001102 r2,0:51,A:49762966;C:48690671;G:46576512;T:56369616;N:8262,51,,,,49762966,48690671,46576512,56369616,8262,SRX23082018,SRS20040786,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29685,SRR27406954,SRX23082017,SRS20040787,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 4 1 [IL 13 30 28],GSM8001101,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 4 1 [IL 13 30 28],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva,GSM8001101,GSM8001101: m 4 1 [IL 13 30 28]; Danio rerio; RNA Seq,GSM8001101 r1,GSM8001101,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-28_TAGCTT_L001_R1_001.fastq.gz,fastq,238045560.0,4667560.0,GSM8001101 r1,0:51,A:58767746;C:57659215;G:55554391;T:66038681;N:25527,51,,,,58767746,57659215,55554391,66038681,25527,SRX23082017,SRS20040787,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29686,SRR27406955,SRX23082017,SRS20040787,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 4 1 [IL 13 30 28],GSM8001101,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 4 1 [IL 13 30 28],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:4 dpf|tissue:whole embryo/larva,GSM8001101,GSM8001101: m 4 1 [IL 13 30 28]; Danio rerio; RNA Seq,GSM8001101 r1,GSM8001101,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-28_TAGCTT_L002_R1_001.fastq.gz,fastq,242904279.0,4762829.0,GSM8001101 r2,0:51,A:60029401;C:58821065;G:56644387;T:67399896;N:9530,51,,,,60029401,58821065,56644387,67399896,9530,SRX23082017,SRS20040787,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29687,SRR27406956,SRX23082016,SRS20040782,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 4 s [IL 13 30 27],GSM8001100,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 4 s [IL 13 30 27],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva,GSM8001100,GSM8001100: p 4 s [IL 13 30 27]; Danio rerio; RNA Seq,GSM8001100 r1,GSM8001100,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-27_GATCAG_L001_R1_001.fastq.gz,fastq,312793965.0,6133215.0,GSM8001100 r1,0:51,A:77247575;C:75189591;G:71777185;T:88544707;N:34907,51,,,,77247575,75189591,71777185,88544707,34907,SRX23082016,SRS20040782,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29688,SRR27406957,SRX23082016,SRS20040782,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 4 s [IL 13 30 27],GSM8001100,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 4 s [IL 13 30 27],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva,GSM8001100,GSM8001100: p 4 s [IL 13 30 27]; Danio rerio; RNA Seq,GSM8001100 r1,GSM8001100,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-27_GATCAG_L002_R1_001.fastq.gz,fastq,317798238.0,6231338.0,GSM8001100 r2,0:51,A:78561371;C:76374371;G:72870754;T:89978216;N:13526,51,,,,78561371,76374371,72870754,89978216,13526,SRX23082016,SRS20040782,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29689,SRR27406958,SRX23082015,SRS20040784,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 4 2 [IL 13 30 26],GSM8001099,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 4 2  [IL 13 30 26],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva,GSM8001099,GSM8001099: p 4 2  [IL 13 30 26]; Danio rerio; RNA Seq,GSM8001099 r1,GSM8001099,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-26_GAGTGG_L001_R1_001.fastq.gz,fastq,358444983.0,7028333.0,GSM8001099 r1,0:51,A:87990429;C:86848774;G:83282005;T:100282103;N:41672,51,,,,87990429,86848774,83282005,100282103,41672,SRX23082015,SRS20040784,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29690,SRR27406959,SRX23082015,SRS20040784,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 4 2 [IL 13 30 26],GSM8001099,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 4 2  [IL 13 30 26],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva,GSM8001099,GSM8001099: p 4 2  [IL 13 30 26]; Danio rerio; RNA Seq,GSM8001099 r1,GSM8001099,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-26_GAGTGG_L002_R1_001.fastq.gz,fastq,363763671.0,7132621.0,GSM8001099 r2,0:51,A:89389622;C:88080819;G:84463019;T:101815021;N:15190,51,,,,89389622,88080819,84463019,101815021,15190,SRX23082015,SRS20040784,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29691,SRR27406960,SRX23082014,SRS20040783,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 4 1 [IL 13 30 25],GSM8001098,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 4 1 [IL 13 30 25],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva,GSM8001098,GSM8001098: p 4 1 [IL 13 30 25]; Danio rerio; RNA Seq,GSM8001098 r1,GSM8001098,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-25_TTAGGC_L001_R1_001.fastq.gz,fastq,264369975.0,5183725.0,GSM8001098 r1,0:51,A:64903076;C:63955314;G:61111702;T:74374447;N:25436,51,,,,64903076,63955314,61111702,74374447,25436,SRX23082014,SRS20040783,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29692,SRR27406961,SRX23082014,SRS20040783,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 4 1 [IL 13 30 25],GSM8001098,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 4 1 [IL 13 30 25],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:4 dpf|tissue:whole embryo/larva,GSM8001098,GSM8001098: p 4 1 [IL 13 30 25]; Danio rerio; RNA Seq,GSM8001098 r1,GSM8001098,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-25_TTAGGC_L002_R1_001.fastq.gz,fastq,268038864.0,5255664.0,GSM8001098 r2,0:51,A:65881878;C:64831975;G:61904001;T:75410447;N:10563,51,,,,65881878,64831975,61904001,75410447,10563,SRX23082014,SRS20040783,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29693,SRR27406962,SRX23082013,SRS20040785,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 5 s [IL 13 30 24],GSM8001097,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:5 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 5 s [IL 13 30 24],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:5 dpf|tissue:whole embryo/larva,GSM8001097,GSM8001097: m 5 s [IL 13 30 24]; Danio rerio; RNA Seq,GSM8001097 r1,GSM8001097,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-24_GCCAAT_L002_R1_001.fastq.gz,fastq,2222118603.0,43570953.0,GSM8001097 r1,0:51,A:576966145;C:539447551;G:521862134;T:583488671;N:354102,51,,,,576966145,539447551,521862134,583488671,354102,SRX23082013,SRS20040785,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29694,SRR27406963,SRX23082012,SRS20040779,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 3 s [IL 13 30 23],GSM8001096,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:3 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 3 s [IL 13 30 23],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:3 dpf|tissue:whole embryo/larva,GSM8001096,GSM8001096: m 3 s [IL 13 30 23]; Danio rerio; RNA Seq,GSM8001096 r1,GSM8001096,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-23_ACAGTG_L002_R1_001.fastq.gz,fastq,1260954855.0,24724605.0,GSM8001096 r1,0:51,A:326961751;C:306257393;G:300159941;T:327374634;N:201136,51,,,,326961751,306257393,300159941,327374634,201136,SRX23082012,SRS20040779,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29695,SRR27406964,SRX23082011,SRS20040777,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 5 s [IL 13 30 22],GSM8001095,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:5 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 5 s [IL 13 30 22],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:5 dpf|tissue:whole embryo/larva,GSM8001095,GSM8001095: p 5 s [IL 13 30 22]; Danio rerio; RNA Seq,GSM8001095 r1,GSM8001095,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-22_TGACCA_L002_R1_001.fastq.gz,fastq,982727262.0,19269162.0,GSM8001095 r1,0:51,A:254210518;C:239327489;G:233438732;T:255593021;N:157502,51,,,,254210518,239327489,233438732,255593021,157502,SRX23082011,SRS20040777,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29696,SRR27406965,SRX23082010,SRS20040778,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 3 s [IL 13 30 21],GSM8001094,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:3 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 3 s [IL 13 30 21],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:3 dpf|tissue:whole embryo/larva,GSM8001094,GSM8001094: p 3 s [IL 13 30 21]; Danio rerio; RNA Seq,GSM8001094 r1,GSM8001094,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-21_CGATGT_L002_R1_001.fastq.gz,fastq,1037356779.0,20340329.0,GSM8001094 r1,0:51,A:269746979;C:251588766;G:245295859;T:270558757;N:166418,51,,,,269746979,251588766,245295859,270558757,166418,SRX23082010,SRS20040778,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29697,SRR27406966,SRX23082009,SRS20040775,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 8 s [IL 13 30 20],GSM8001093,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:8 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 8 s [IL 13 30 20],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:8 dpf|tissue:whole embryo/larva,GSM8001093,GSM8001093: m 8 s [IL 13 30 20]; Danio rerio; RNA Seq,GSM8001093 r1,GSM8001093,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-20_GGCTAC_L002_R1_001.fastq.gz,fastq,553647228.0,10855828.0,GSM8001093 r1,0:51,A:134883646;C:143513277;G:139480793;T:135331042;N:438470,51,,,,134883646,143513277,139480793,135331042,438470,SRX23082009,SRS20040775,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29698,SRR27406967,SRX23082008,SRS20040776,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,M 8 1 [IL 13 30 19],GSM8001092,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:8 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,M 8 1 [IL 13 30 19],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:8 dpf|tissue:whole embryo/larva,GSM8001092,GSM8001092: M 8 1 [IL 13 30 19]; Danio rerio; RNA Seq,GSM8001092 r1,GSM8001092,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-19_TAGCTT_L002_R1_001.fastq.gz,fastq,62964855.0,1234605.0,GSM8001092 r1,0:51,A:15317447;C:16365148;G:15892573;T:15339413;N:50274,51,,,,15317447,16365148,15892573,15339413,50274,SRX23082008,SRS20040776,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29699,SRR27406968,SRX23082008,SRS20040776,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,M 8 1 [IL 13 30 19],GSM8001092,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:8 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,M 8 1 [IL 13 30 19],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:8 dpf|tissue:whole embryo/larva,GSM8001092,GSM8001092: M 8 1 [IL 13 30 19]; Danio rerio; RNA Seq,GSM8001092 r1,GSM8001092,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-19_TAGCTT_L002_R1_002.fastq.gz,fastq,819926286.0,16076986.0,GSM8001092 r2,0:51,A:200506200;C:212085852;G:207134817;T:200070297;N:129120,51,,,,200506200,212085852,207134817,200070297,129120,SRX23082008,SRS20040776,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29700,SRR27406969,SRX23082007,SRS20040780,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 8 s [IL 13 30 18],GSM8001091,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:8 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 8 s [IL 13 30 18],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:8 dpf|tissue:whole embryo/larva,GSM8001091,GSM8001091: p 8 s [IL 13 30 18]; Danio rerio; RNA Seq,GSM8001091 r1,GSM8001091,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-18_GATCAG_L002_R1_001.fastq.gz,fastq,639923316.0,12547516.0,GSM8001091 r1,0:51,A:163788580;C:157878572;G:152810290;T:164930630;N:515244,51,,,,163788580,157878572,152810290,164930630,515244,SRX23082007,SRS20040780,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29701,SRR27406970,SRX23082006,SRS20040781,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 8 1 [IL 13 30 17],GSM8001090,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:8 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 8 1 [IL 13 30 17],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:8 dpf|tissue:whole embryo/larva,GSM8001090,GSM8001090: p 8 1 [IL 13 30 17]; Danio rerio; RNA Seq,GSM8001090 r1,GSM8001090,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-17_ACTTGA_L002_R1_001.fastq.gz,fastq,586754847.0,11504997.0,GSM8001090 r1,0:51,A:144643558;C:150218708;G:146661023;T:144769661;N:461897,51,,,,144643558,150218708,146661023,144769661,461897,SRX23082006,SRS20040781,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29702,SRR27406971,SRX23082005,SRS20040774,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 6 s [IL 13 30 16],GSM8001089,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:6 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 6 s [IL 13 30 16],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:6 dpf|tissue:whole embryo/larva,GSM8001089,GSM8001089: m 6 s [IL 13 30 16]; Danio rerio; RNA Seq,GSM8001089 r1,GSM8001089,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-16_TTAGGC_L002_R1_001.fastq.gz,fastq,443064948.0,8687548.0,GSM8001089 r1,0:51,A:111215571;C:111682539;G:108653697;T:111157539;N:355602,51,,,,111215571,111682539,108653697,111157539,355602,SRX23082005,SRS20040774,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29703,SRR27406972,SRX23082004,SRS20040773,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 6 1 [IL 13 30 15],GSM8001088,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:6 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 6 1 [IL 13 30 15],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:6 dpf|tissue:whole embryo/larva,GSM8001088,GSM8001088: m 6 1 [IL 13 30 15]; Danio rerio; RNA Seq,GSM8001088 r1,GSM8001088,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-15_ATCACG_L002_R1_001.fastq.gz,fastq,882129252.0,17296652.0,GSM8001088 r1,0:51,A:232882429;C:211887994;G:201698856;T:234945732;N:714241,51,,,,232882429,211887994,201698856,234945732,714241,SRX23082004,SRS20040773,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29704,SRR27406973,SRX23082003,SRS20040770,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 6 2 [IL 13 30 14],GSM8001087,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:6 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 6 2 [IL 13 30 14],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:6 dpf|tissue:whole embryo/larva,GSM8001087,GSM8001087: p 6 2 [IL 13 30 14]; Danio rerio; RNA Seq,GSM8001087 r1,GSM8001087,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-14_GTGAAA_L002_R1_001.fastq.gz,fastq,547226022.0,10729922.0,GSM8001087 r1,0:51,A:132788152;C:142246667;G:138933647;T:132816349;N:441207,51,,,,132788152,142246667,138933647,132816349,441207,SRX23082003,SRS20040770,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29705,SRR27406974,SRX23082002,SRS20040769,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 6 1 [IL 13 30 13],GSM8001086,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:6 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 6 1 [IL 13 30 13],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:6 dpf|tissue:whole embryo/larva,GSM8001086,GSM8001086: p 6 1 [IL 13 30 13]; Danio rerio; RNA Seq,GSM8001086 r1,GSM8001086,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-13_GTCCGC_L002_R1_001.fastq.gz,fastq,520266810.0,10201310.0,GSM8001086 r1,0:51,A:125933056;C:135555201;G:132217921;T:126145133;N:415499,51,,,,125933056,135555201,132217921,126145133,415499,SRX23082002,SRS20040769,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29706,SRR27406975,SRX23082001,SRS20040772,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 5 2 [IL 13 30 12],GSM8001085,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:5 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 5 2 [IL 13 30 12],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:5 dpf|tissue:whole embryo/larva,GSM8001085,GSM8001085: m 5 2 [IL 13 30 12]; Danio rerio; RNA Seq,GSM8001085 r1,GSM8001085,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-12_CCGTCC_L002_R1_001.fastq.gz,fastq,580544118.0,11383218.0,GSM8001085 r1,0:51,A:147287127;C:144405857;G:140535839;T:147847352;N:467943,51,,,,147287127,144405857,140535839,147847352,467943,SRX23082001,SRS20040772,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29707,SRR27406976,SRX23082000,SRS20040771,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 5 1 [IL 13 30 11],GSM8001084,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:5 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 5 1 [IL 13 30 11],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:5 dpf|tissue:whole embryo/larva,GSM8001084,GSM8001084: m 5 1 [IL 13 30 11]; Danio rerio; RNA Seq,GSM8001084 r1,GSM8001084,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-11_ATGTCA_L002_R1_001.fastq.gz,fastq,575366394.0,11281694.0,GSM8001084 r1,0:51,A:149073331;C:140502112;G:136425599;T:148905317;N:460035,51,,,,149073331,140502112,136425599,148905317,460035,SRX23082000,SRS20040771,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29708,SRR27406977,SRX23081999,SRS20040767,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 5 2 [IL 13 30 10],GSM8001083,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:5 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 5 2 [IL 13 30 10],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:5 dpf|tissue:whole embryo/larva,GSM8001083,GSM8001083: p 5 2 [IL 13 30 10]; Danio rerio; RNA Seq,GSM8001083 r1,GSM8001083,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-10_AGTTCC_L001_R1_001.fastq.gz,fastq,542919888.0,10645488.0,GSM8001083 r1,0:51,A:138706445;C:133885327;G:130561786;T:139292916;N:473414,51,,,,138706445,133885327,130561786,139292916,473414,SRX23081999,SRS20040767,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29709,SRR27406978,SRX23081998,SRS20040768,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 5 1 [IL 13 30 9],GSM8001082,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:5 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 5 1 [IL 13 30 9],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:5 dpf|tissue:whole embryo/larva,GSM8001082,GSM8001082: p 5 1 [IL 13 30 9]; Danio rerio; RNA Seq,GSM8001082 r1,GSM8001082,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-9_AGTCAA_L001_R1_001.fastq.gz,fastq,452635557.0,8875207.0,GSM8001082 r1,0:51,A:116752949;C:110829948;G:107471046;T:117187118;N:394496,51,,,,116752949,110829948,107471046,117187118,394496,SRX23081998,SRS20040768,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29710,SRR27406979,SRX23081997,SRS20040765,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 3 2 [IL 13 30 8],GSM8001081,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:3 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 3 2 [IL 13 30 8],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:3 dpf|tissue:whole embryo/larva,GSM8001081,GSM8001081: m 3 2 [IL 13 30 8]; Danio rerio; RNA Seq,GSM8001081 r1,GSM8001081,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-8_CTTGTA_L001_R1_001.fastq.gz,fastq,489962100.0,9607100.0,GSM8001081 r1,0:51,A:126576626;C:120177833;G:115721569;T:127054827;N:431245,51,,,,126576626,120177833,115721569,127054827,431245,SRX23081997,SRS20040765,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29711,SRR27406980,SRX23081996,SRS20040763,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m3 1 [IL 13 30 7],GSM8001080,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:3 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m3 1 [IL 13 30 7],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:3 dpf|tissue:whole embryo/larva,GSM8001080,GSM8001080: m3 1 [IL 13 30 7]; Danio rerio; RNA Seq,GSM8001080 r1,GSM8001080,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-7_CAGATC_L001_R1_001.fastq.gz,fastq,508392072.0,9968472.0,GSM8001080 r1,0:51,A:131266675;C:124519771;G:120906726;T:131244280;N:454620,51,,,,131266675,124519771,120906726,131244280,454620,SRX23081996,SRS20040763,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29712,SRR27406981,SRX23081995,SRS20040762,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 3 2 [IL 13 30 6],GSM8001079,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:3 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 3 2 [IL 13 30 6],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:3 dpf|tissue:whole embryo/larva,GSM8001079,GSM8001079: p 3 2 [IL 13 30 6]; Danio rerio; RNA Seq,GSM8001079 r1,GSM8001079,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-6_GCCAAT_L001_R1_001.fastq.gz,fastq,453386736.0,8889936.0,GSM8001079 r1,0:51,A:116163394;C:112054233;G:108633583;T:116138053;N:397473,51,,,,116163394,112054233,108633583,116138053,397473,SRX23081995,SRS20040762,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29713,SRR27406982,SRX23081994,SRS20040761,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 3 1 [IL 13 30 5],GSM8001078,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:3 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 3 1 [IL 13 30 5],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:3 dpf|tissue:whole embryo/larva,GSM8001078,GSM8001078: p 3 1 [IL 13 30 5]; Danio rerio; RNA Seq,GSM8001078 r1,GSM8001078,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-5_ACAGTG_L001_R1_001.fastq.gz,fastq,527854335.0,10350085.0,GSM8001078 r1,0:51,A:136133452;C:129943239;G:125251939;T:136062979;N:462726,51,,,,136133452,129943239,125251939,136062979,462726,SRX23081994,SRS20040761,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29714,SRR27406983,SRX23081993,SRS20040766,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 0 s [IL 13 30 4],GSM8001077,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:0 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 0 s [IL 13 30 4],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:0 dpf|tissue:whole embryo/larva,GSM8001077,GSM8001077: m 0 s [IL 13 30 4]; Danio rerio; RNA Seq,GSM8001077 r1,GSM8001077,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-4_TGACCA_L001_R1_001.fastq.gz,fastq,498889140.0,9782140.0,GSM8001077 r1,0:51,A:129822030;C:121205451;G:117439534;T:129980097;N:442028,51,,,,129822030,121205451,117439534,129980097,442028,SRX23081993,SRS20040766,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29715,SRR27406984,SRX23081992,SRS20040764,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,m 0 1 [IL 13 30 3],GSM8001076,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:0 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,m 0 1 [IL 13 30 3],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:Mtb in PVP|time:0 dpf|tissue:whole embryo/larva,GSM8001076,GSM8001076: m 0 1 [IL 13 30 3]; Danio rerio; RNA Seq,GSM8001076 r1,GSM8001076,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-3_CGATGT_L001_R1_001.fastq.gz,fastq,555321507.0,10888657.0,GSM8001076 r1,0:51,A:146330990;C:133169384;G:129452235;T:145880324;N:488574,51,,,,146330990,133169384,129452235,145880324,488574,SRX23081992,SRS20040764,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29716,SRR27406985,SRX23081991,SRS20040760,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 0 2 [IL 13 30 2],GSM8001075,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:0 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 0 2 [IL 13 30 2],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:0 dpf|tissue:whole embryo/larva,GSM8001075,GSM8001075: p 0 2 [IL 13 30 2]; Danio rerio; RNA Seq,GSM8001075 r1,GSM8001075,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-2_ATTCCT_L001_R1_001.fastq.gz,fastq,597771663.0,11721013.0,GSM8001075 r1,0:51,A:158875230;C:142332785;G:137965987;T:158067772;N:529889,51,,,,158875230,142332785,137965987,158067772,529889,SRX23081991,SRS20040760,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
29717,SRR27406986,SRX23081990,SRS20040759,SRP481061,PRJNA1060611,The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger the same core set of late immune response genes in zebrafish larvae,GSE252417,Transcriptome Analysis,Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum M. marinum is evolutionarily most closely related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen  we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNAseq. Granuloma like structures carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post infection. The continued presence of viable M. tuberculosis in the zebrafish larvae was further confirmed using the molecular bacterial load assay. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week post infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. Overall design: To study the effect of Mycobacterium tuberculosis Mtb infection on gene expression in zebrafish larvae  early embryos were robotically injected into the yolk with Mtb H37rv Berlin strain in PVP or with PVP alone. Embryos/larvae were harvested at 0  1  2  3  4  5  6  8 dpf and 9 dpf dpf and used for total RNA extraction. RNA samples derived from 0  3  4  5  6  and 8 dpf samples were used for Illumina RNA sequencing. Differential gene expression analysis was performed by comparing Mtb infected samples with PVP infected control samples in triplo; except for 8 dpf  which was in duplo.,,,,p 0 1 [IL 13 30 1],GSM8001074,,source name:whole embryo/larva|strain:AB/TL|genotype:wild type|treatment:PVP al1|time:0 dpf|tissue:whole embryo/larva|geo loc name:missing|collection date:missing,p 0 1 [IL 13 30 1],"GeneTiles Veneman et al.  2015; Immunogenetics 67  135 147 Bowtie2 was used to align the reads to the reference genome Danio rerio GRCz11. Samtools was used to convert SAM to BAM and to sort reads. Aligned reads were counted using Htseq and pysam. DESeq was used to perform statistical analysis of differentially expressed genes. Assembly: GRCz11 Supplementary files format and content: Microsoft Office Excel file .xlsx with the following columns: chromosome; gene;  Ensembl gene id; Entrez gene id; baseMean; GO accessions; Human homologs; library name ""raw"" and ""scaled"" for each ctrl and Mtb sample; MEAN ctrl value; MEAN Mtb value; MEAS/CTRL or  CTRL/MEAS scaled; p value; adjusted p value; best exon p value",whole embryo/larva,16 128 cell stage embryos were robotically injected into the yolk with 500 CFU of Mtb H37Rv in PVP or with PVP alone.,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,AB/TL zebrafish embryos/larvae were incubated at 34 degrees celsius.,strain:AB/TL|genotype:wild type|treatment:PVP al1|time:0 dpf|tissue:whole embryo/larva,GSM8001074,GSM8001074: p 0 1 [IL 13 30 1]; Danio rerio; RNA Seq,GSM8001074 r1,GSM8001074,1,Total RNA was extracted using Qiagen's miRNeasy mini kit. RNAseq libraries were prepared from 2 ug total RNA using Illumina's TruSeq RNA sample prep kit version 2.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP481061,,,IL-13-30-1_ACTGAT_L001_R1_001.fastq.gz,fastq,501543843.0,9834193.0,GSM8001074 r1,0:51,A:132665355;C:120159464;G:115900014;T:132380562;N:438448,51,,,,132665355,120159464,115900014,132380562,438448,SRX23081990,SRS20040759,SRA1779138,Future Genomics Technologies BV,Future Genomics Technologies BV,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2024-01-03,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
30006,SRR27663958,SRX23331822,SRS20194274,SRP484810,PRJNA1066877,p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation,GSE253758,Transcriptome Analysis,While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.,,pubmed:39242546,,NFKB   biol rep 3,GSM8027552,,tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted|geo loc name:missing|collection date:missing,NFKB   biol rep 3,Data was analyzed by ROSALIND® https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene,endothelial cells,22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.,cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted,GSM8027552,GSM8027552: NFKB   biol rep 3; Danio rerio; RNA Seq,GSM8027552 r1,GSM8027552,1,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484810,,loader:fastq load.py,6-RNA-1001_S6_L001_R1_001.fastq.gz,fastq,7566894200.0,75668942.0,GSM8027552 r1,0:100,A:2055514007;C:1776454819;G:1779667416;T:1955100553;N:157405,100,,,,2055514007,1776454819,1779667416,1955100553,157405,SRX23331822,SRS20194274,SRA1788753,Iowa State University,Iowa State University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-01-19,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
30007,SRR27663959,SRX23331821,SRS20194275,SRP484810,PRJNA1066877,p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation,GSE253758,Transcriptome Analysis,While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.,,pubmed:39242546,,NFKB   biol rep 2,GSM8027551,,tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted|geo loc name:missing|collection date:missing,NFKB   biol rep 2,Data was analyzed by ROSALIND® https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene,endothelial cells,22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.,cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted,GSM8027551,GSM8027551: NFKB   biol rep 2; Danio rerio; RNA Seq,GSM8027551 r1,GSM8027551,1,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484810,,loader:fastq load.py,5-RNA-0901_S5_L001_R1_001.fastq.gz,fastq,8077393600.0,80773936.0,GSM8027551 r1,0:100,A:2195547260;C:1863472493;G:1887149224;T:2131055526;N:169097,100,,,,2195547260,1863472493,1887149224,2131055526,169097,SRX23331821,SRS20194275,SRA1788753,Iowa State University,Iowa State University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-01-19,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
30008,SRR27663960,SRX23331820,SRS20194273,SRP484810,PRJNA1066877,p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation,GSE253758,Transcriptome Analysis,While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.,,pubmed:39242546,,NFKB   biol rep 1,GSM8027550,,tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted|geo loc name:missing|collection date:missing,NFKB   biol rep 1,Data was analyzed by ROSALIND® https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene,endothelial cells,22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.,cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted,GSM8027550,GSM8027550: NFKB   biol rep 1; Danio rerio; RNA Seq,GSM8027550 r1,GSM8027550,1,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484810,,loader:fastq load.py,4-RNA-1001_S4_L001_R1_001.fastq.gz,fastq,6536957300.0,65369573.0,GSM8027550 r1,0:100,A:1764502914;C:1531091007;G:1533764634;T:1707464708;N:134037,100,,,,1764502914,1531091007,1533764634,1707464708,134037,SRX23331820,SRS20194273,SRA1788753,Iowa State University,Iowa State University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-01-19,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
30009,SRR27663961,SRX23331819,SRS20194272,SRP484810,PRJNA1066877,p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation,GSE253758,Transcriptome Analysis,While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.,,pubmed:39242546,,NFKB+  biol rep 3,GSM8027549,,tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted|geo loc name:missing|collection date:missing,NFKB+  biol rep 3,Data was analyzed by ROSALIND® https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene,endothelial cells,22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.,cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted,GSM8027549,GSM8027549: NFKB+  biol rep 3; Danio rerio; RNA Seq,GSM8027549 r1,GSM8027549,1,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484810,,loader:fastq load.py,3-RNA-1001_S3_L001_R1_001.fastq.gz,fastq,10375249700.0,103752497.0,GSM8027549 r1,0:100,A:2873369145;C:2335823279;G:2356855554;T:2808985435;N:216287,100,,,,2873369145,2335823279,2356855554,2808985435,216287,SRX23331819,SRS20194272,SRA1788753,Iowa State University,Iowa State University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-01-19,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
30010,SRR27663962,SRX23331818,SRS20194271,SRP484810,PRJNA1066877,p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation,GSE253758,Transcriptome Analysis,While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.,,pubmed:39242546,,NFKB+  biol rep 2,GSM8027548,,tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted|geo loc name:missing|collection date:missing,NFKB+  biol rep 2,Data was analyzed by ROSALIND® https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene,endothelial cells,22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.,cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted,GSM8027548,GSM8027548: NFKB+  biol rep 2; Danio rerio; RNA Seq,GSM8027548 r1,GSM8027548,1,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484810,,loader:fastq load.py,2-RNA-1001_S2_L001_R1_001.fastq.gz,fastq,5743794100.0,57437941.0,GSM8027548 r1,0:100,A:1588561398;C:1297479370;G:1310669617;T:1546965673;N:118042,100,,,,1588561398,1297479370,1310669617,1546965673,118042,SRX23331818,SRS20194271,SRA1788753,Iowa State University,Iowa State University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-01-19,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
30011,SRR27663963,SRX23331817,SRS20194270,SRP484810,PRJNA1066877,p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation,GSE253758,Transcriptome Analysis,While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.,,pubmed:39242546,,NFKB+  biol rep 1,GSM8027547,,tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted|geo loc name:missing|collection date:missing,NFKB+  biol rep 1,Data was analyzed by ROSALIND® https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene,endothelial cells,22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.,cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted,GSM8027547,GSM8027547: NFKB+  biol rep 1; Danio rerio; RNA Seq,GSM8027547 r1,GSM8027547,1,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484810,,loader:fastq load.py,1-RNA-0917_S1_L001_R1_001.fastq.gz,fastq,6201542500.0,62015425.0,GSM8027547 r1,0:100,A:1696049302;C:1431941155;G:1441395671;T:1632027072;N:129300,100,,,,1696049302,1431941155,1441395671,1632027072,129300,SRX23331817,SRS20194270,SRA1788753,Iowa State University,Iowa State University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-01-19,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
30658,SRR28054753,SRX23704452,SRS20534448,SRP491086,PRJNA1078753,Integrated mRNA  and miRNA  sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos,PRJNA1078753,Other,Tobacco pollutants are prevalent in the environment  leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore  in this study  we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25%  1%  and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity  including increased mortality and decreased incubation rate  in a dose dependent manner. Moreover  CSE induced malformations and apoptosis  specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment  apoptosis disorder  and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis  and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.,,,,,S21K1230,,library ID:H 3|title:High 3|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1230 rep1 1 URNA S74 L003 R1 001.fastq|filename2:S21K1230 rep1 1 URNA S74 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal,,,,,,,,,High 3,H 3,H 3,missing,,,RNA-Seq,METATRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP491086,,,S21K1230_rep1_1_URNA_S74_L003_R1_001.fastq.gz S21K1230_rep1_1_URNA_S74_L003_R2_001.fastq.gz,fastq fastq,6117817800.0,20392726.0,S21K1230 rep1 1 URNA S74 L003 R1 001.fastq.gz,0:150 1:150,A:1635728688;C:1405168032;G:1464072107;T:1612834762;N:14211,150,150,,,1635728688,1405168032,1464072107,1612834762,14211,SRX23704452,SRS20534448,SRA1806456,The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery,The Second Affiliated Hospital of Shantou University Medical College,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,China,2024-02-22,Undetermined,Multi-stage,Undetermined,Undetermined
30691,SRR28270998,SRX23880961,SRS20704477,SRP494117,PRJNA1085662,Roxithromycin exposure induces motoneuron malformation and behavioral deficits of zebrafish by interfering with the differentiation of motor neuron progenitor cells,PRJNA1085662,Other,Roxithromycin ROX  a commonly used macrolide antibiotic  is extensively employed in human medicine and livestock industries. Due to its structural stability and resistance to biological degradation  ROX persists as a resilient environmental contaminant  detectable in aquatic ecosystems and food products. However  our understanding of the potential health risks to humans from continuous ROX exposure remains limited. In this study  we used the zebrafish as a vertebrate model to explore the potential developmental toxicity of early ROX exposure  particularly focusing on its effects on locomotor functionality and motoneuron development. Early exposure to ROX induces marked developmental toxicity in zebrafish embryos  significantly reducing hatch rates  body lengths  and increased malformation rates. Moreover  ROX exposure adversely affected the locomotive capacity of zebrafish embryos  and observations in transgenic zebrafish Tghb9:eGFP revealed axonal loss in motor neurons  evident through reduced or irregular axonal lengths. Concurrently  abnormal apoptosis in ROX exposed zebrafish embryos intensified alongside the upregulation of apoptosis related genes bax  bcl2  caspase 3a. Single cell sequencing further disclosed substantial effects of ROX on genes involved in the differentiation of motor neuron progenitor cells ngn1  olig2  axon development cd82a  mbpa  plp1b  sema5a  and neuroimmunity aplnrb  aplnra in zebrafish larvae. Furthermore  the motor neuron defects induced by ROX can be rescued by administering ngn1 agonist. In summary  ROX exposure leads to early life abnormalities in zebrafish motor neurons and locomotor behavior by hindering the differentiation of motor neuron progenitor cells and inducing abnormal apoptosis.,,,,,WT,,strain:not provided|isolate:not provided|breed:not provided|cultivar:not provided|ecotype:not provided|age:not provided|dev stage:not provided|collection date:not provided|geo loc name:not provided|sex:not provided|tissue:Cerebrum|BioSampleModel:Model organism or animal,,,,,,,,,Roxithromycin exposure induces mot1uron malformation and behavioral deficits of zebrafish by interfering with the differentiation of motor neuron progenitor cells,DANIO,DANIO,Illumina Second Generation Sequencing,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,SINGLE,BGISEQ,BGISEQ-500,,SRP494117,,,WT_S1_L001_I1_001.fastq.gz,fastq,7991376264.0,998922033.0,WT S1 L001 I1 001.fastq.gz,0:8,A:2573734851;C:1426474966;G:1492966198;T:2498173074;N:27175,8,,,,2573734851,1426474966,1492966198,2498173074,27175,SRX23880961,SRS20704477,SRA1820072,shantou university|Neurobiology Center,shantou university,1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,bgi,bgi,unknown,poly_a,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-03-11,Undetermined,Multi-stage,Brain,Nervous System
33659,SRR30476759,SRX25901727,SRS22493412,SRP529442,PRJNA1154244,ZNF574 is a Quality Control Factor for Defective Ribosome Biogenesis Intermediates [RNA Seq],GSE275992,Transcriptome Analysis,Eukaryotic ribosome assembly is an intricate process that involves four ribosomal RNAs  80 ribosomal proteins  and over 200 biogenesis factors that take part in numerous interdependent steps. The complexity and essentiality of this process creates opportunities for deleterious mutations to occur  accumulate  and impact downstream cellular processes. “Dead end” ribosome intermediates that result from biogenesis errors are rapidly degraded  affirming the existence of quality control pathways that monitor ribosome assembly. However  the factors that differentiate between on path and dead end intermediates are unknown. We engineered a system to perturb ribosome assembly in human cells and discovered that faulty ribosomes are degraded via the ubiquitin proteasome system. We identified ZNF574 as a key component of a novel quality control pathway  which we term the Ribosome Assembly Surveillance Pathway RASP. In an animal model  loss of ZNF574 leads to developmental defects  further emphasizing the importance of RASP in organismal health. Overall design: To identify differentially expressed genes following the loss of znf574  we in crossed znf574+/  animals. znf574 wild type znf574+/+ or +/  and znf574 mutant znf574 /  larvae were phenotypically identified seven dpf Whole animals were used for this experiment. We performed RNA Seq followed by differential expression analysis with DESeq2  comparing differentially expressed genes between ZNF574 mutant and wild type animals.,,pubmed:40328246,,Whole Body Mut R2,GSM8489057,,tissue:whole larvae|cell line:whole larvae|cell type:all cell types|genotype:znf574 / |treatment:N1|time:NA|geo loc name:missing|collection date:missing,Whole Body Mut R2,Reads were de multiplexed using Illumina’s bcl2fastq v2.20. Reads were aligned to the zebrafish genome GRCz11/danRer11 using kallisto v0.46.0. DESeq2 Galaxy Version 2.11.40+galaxy2 was used for differential expression analysis Genes with a minimum two fold upregulation in znf574 /  larvae and an adjusted p value of less than 0.05 were selected for further analysis. Pathway analysis was performed using the Kyoto Encyclopedia of Genes and Genomes database KEGG www.genome.jp/kegg. Pathway enrichment analyses were performed by using the Database for Annotation  Visualization and Integrated Discovery DAVID Bioinformatics  https://david.ncifcrf.gov/tools.jsp. Assembly: GRCz11/danRer11 Supplementary files format and content: tab separated value file that includes the raw count for each sample,whole larvae,znf574+/  heterozygous animals were in crossed  and fertilized eggs were collected and maintained in a zebrafish incubator for 8 days. Water was exchanged daily. Seven dpf  znf574 mutant animals can be easily distinguished from wild type siblings.,RNA from whole animals was extracted using phenol/chloroform isoamyl alcohol extraction. Libraries were cloned using Illumina TruSeq® Stranded mRNA Library Prep 20020595.,Adult zebrafish were maintained on a 14 h light–10 h dark cycle and fed once daily with 3.5% body weight of Gemma Micro 500 Skretting USA. All genotypes were bred into the wild type AB background.  All procedures comply with all relevant ethical regulations and were approved by the Carnegie Institution Animal Care and Use Committee Protocol #162 and the animal ethics committee IACUC review board at the Stowers Institute for MedicalResearch Protocol #2024 171.,cell line:whole larvae|cell type:all cell types|genotype:znf574 / |treatment:N1|time:NA,GSM8489057,GSM8489057: Whole Body Mut R2; Danio rerio; RNA Seq,GSM8489057 r1,GSM8489057,1,RNA from whole animals was extracted using phenol/chloroform isoamyl alcohol extraction. Libraries were cloned using Illumina TruSeq® Stranded mRNA Library Prep 20020595.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP529442,,,6_Whole_Body_Mutant_S8_L004_R1_001.fastq.gz,fastq,766293825.0,10217251.0,GSM8489057 r1,0:75,A:194461148;C:175434886;G:181181789;T:215200139;N:15863,75,,,,194461148,175434886,181181789,215200139,15863,SRX25901727,SRS22493412,SRA1958985,Stowers Institute for Medical Research,Stowers Institute for Medical Research,1,0.96072,,0.1396,,0.66892,,0.47985,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2024-08-29,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
33660,SRR30476760,SRX25901726,SRS22493410,SRP529442,PRJNA1154244,ZNF574 is a Quality Control Factor for Defective Ribosome Biogenesis Intermediates [RNA Seq],GSE275992,Transcriptome Analysis,Eukaryotic ribosome assembly is an intricate process that involves four ribosomal RNAs  80 ribosomal proteins  and over 200 biogenesis factors that take part in numerous interdependent steps. The complexity and essentiality of this process creates opportunities for deleterious mutations to occur  accumulate  and impact downstream cellular processes. “Dead end” ribosome intermediates that result from biogenesis errors are rapidly degraded  affirming the existence of quality control pathways that monitor ribosome assembly. However  the factors that differentiate between on path and dead end intermediates are unknown. We engineered a system to perturb ribosome assembly in human cells and discovered that faulty ribosomes are degraded via the ubiquitin proteasome system. We identified ZNF574 as a key component of a novel quality control pathway  which we term the Ribosome Assembly Surveillance Pathway RASP. In an animal model  loss of ZNF574 leads to developmental defects  further emphasizing the importance of RASP in organismal health. Overall design: To identify differentially expressed genes following the loss of znf574  we in crossed znf574+/  animals. znf574 wild type znf574+/+ or +/  and znf574 mutant znf574 /  larvae were phenotypically identified seven dpf Whole animals were used for this experiment. We performed RNA Seq followed by differential expression analysis with DESeq2  comparing differentially expressed genes between ZNF574 mutant and wild type animals.,,pubmed:40328246,,Whole Body Mut R1,GSM8489056,,tissue:whole larvae|cell line:whole larvae|cell type:all cell types|genotype:znf574 / |treatment:N1|time:NA|geo loc name:missing|collection date:missing,Whole Body Mut R1,Reads were de multiplexed using Illumina’s bcl2fastq v2.20. Reads were aligned to the zebrafish genome GRCz11/danRer11 using kallisto v0.46.0. DESeq2 Galaxy Version 2.11.40+galaxy2 was used for differential expression analysis Genes with a minimum two fold upregulation in znf574 /  larvae and an adjusted p value of less than 0.05 were selected for further analysis. Pathway analysis was performed using the Kyoto Encyclopedia of Genes and Genomes database KEGG www.genome.jp/kegg. Pathway enrichment analyses were performed by using the Database for Annotation  Visualization and Integrated Discovery DAVID Bioinformatics  https://david.ncifcrf.gov/tools.jsp. Assembly: GRCz11/danRer11 Supplementary files format and content: tab separated value file that includes the raw count for each sample,whole larvae,znf574+/  heterozygous animals were in crossed  and fertilized eggs were collected and maintained in a zebrafish incubator for 8 days. Water was exchanged daily. Seven dpf  znf574 mutant animals can be easily distinguished from wild type siblings.,RNA from whole animals was extracted using phenol/chloroform isoamyl alcohol extraction. Libraries were cloned using Illumina TruSeq® Stranded mRNA Library Prep 20020595.,Adult zebrafish were maintained on a 14 h light–10 h dark cycle and fed once daily with 3.5% body weight of Gemma Micro 500 Skretting USA. All genotypes were bred into the wild type AB background.  All procedures comply with all relevant ethical regulations and were approved by the Carnegie Institution Animal Care and Use Committee Protocol #162 and the animal ethics committee IACUC review board at the Stowers Institute for MedicalResearch Protocol #2024 171.,cell line:whole larvae|cell type:all cell types|genotype:znf574 / |treatment:N1|time:NA,GSM8489056,GSM8489056: Whole Body Mut R1; Danio rerio; RNA Seq,GSM8489056 r1,GSM8489056,1,RNA from whole animals was extracted using phenol/chloroform isoamyl alcohol extraction. Libraries were cloned using Illumina TruSeq® Stranded mRNA Library Prep 20020595.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP529442,,,5_Whole_Body_Mutant_S7_L004_R1_001.fastq.gz,fastq,1009914675.0,13465529.0,GSM8489056 r1,0:75,A:264936373;C:234863581;G:224584569;T:285509610;N:20542,75,,,,264936373,234863581,224584569,285509610,20542,SRX25901726,SRS22493410,SRA1958985,Stowers Institute for Medical Research,Stowers Institute for Medical Research,1,0.95446,,0.12713,,0.66436,,0.47956,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2024-08-29,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
33661,SRR30476761,SRX25901725,SRS22493411,SRP529442,PRJNA1154244,ZNF574 is a Quality Control Factor for Defective Ribosome Biogenesis Intermediates [RNA Seq],GSE275992,Transcriptome Analysis,Eukaryotic ribosome assembly is an intricate process that involves four ribosomal RNAs  80 ribosomal proteins  and over 200 biogenesis factors that take part in numerous interdependent steps. The complexity and essentiality of this process creates opportunities for deleterious mutations to occur  accumulate  and impact downstream cellular processes. “Dead end” ribosome intermediates that result from biogenesis errors are rapidly degraded  affirming the existence of quality control pathways that monitor ribosome assembly. However  the factors that differentiate between on path and dead end intermediates are unknown. We engineered a system to perturb ribosome assembly in human cells and discovered that faulty ribosomes are degraded via the ubiquitin proteasome system. We identified ZNF574 as a key component of a novel quality control pathway  which we term the Ribosome Assembly Surveillance Pathway RASP. In an animal model  loss of ZNF574 leads to developmental defects  further emphasizing the importance of RASP in organismal health. Overall design: To identify differentially expressed genes following the loss of znf574  we in crossed znf574+/  animals. znf574 wild type znf574+/+ or +/  and znf574 mutant znf574 /  larvae were phenotypically identified seven dpf Whole animals were used for this experiment. We performed RNA Seq followed by differential expression analysis with DESeq2  comparing differentially expressed genes between ZNF574 mutant and wild type animals.,,pubmed:40328246,,Whole Body WT R2,GSM8489055,,tissue:whole larvae|cell line:whole larvae|cell type:all cell types|genotype:znf574+/+ or znf574+/ |treatment:N1|time:NA|geo loc name:missing|collection date:missing,Whole Body WT R2,Reads were de multiplexed using Illumina’s bcl2fastq v2.20. Reads were aligned to the zebrafish genome GRCz11/danRer11 using kallisto v0.46.0. DESeq2 Galaxy Version 2.11.40+galaxy2 was used for differential expression analysis Genes with a minimum two fold upregulation in znf574 /  larvae and an adjusted p value of less than 0.05 were selected for further analysis. Pathway analysis was performed using the Kyoto Encyclopedia of Genes and Genomes database KEGG www.genome.jp/kegg. Pathway enrichment analyses were performed by using the Database for Annotation  Visualization and Integrated Discovery DAVID Bioinformatics  https://david.ncifcrf.gov/tools.jsp. Assembly: GRCz11/danRer11 Supplementary files format and content: tab separated value file that includes the raw count for each sample,whole larvae,znf574+/  heterozygous animals were in crossed  and fertilized eggs were collected and maintained in a zebrafish incubator for 8 days. Water was exchanged daily. Seven dpf  znf574 mutant animals can be easily distinguished from wild type siblings.,RNA from whole animals was extracted using phenol/chloroform isoamyl alcohol extraction. Libraries were cloned using Illumina TruSeq® Stranded mRNA Library Prep 20020595.,Adult zebrafish were maintained on a 14 h light–10 h dark cycle and fed once daily with 3.5% body weight of Gemma Micro 500 Skretting USA. All genotypes were bred into the wild type AB background.  All procedures comply with all relevant ethical regulations and were approved by the Carnegie Institution Animal Care and Use Committee Protocol #162 and the animal ethics committee IACUC review board at the Stowers Institute for MedicalResearch Protocol #2024 171.,cell line:whole larvae|cell type:all cell types|genotype:znf574+/+ or znf574+/ |treatment:N1|time:NA,GSM8489055,GSM8489055: Whole Body WT R2; Danio rerio; RNA Seq,GSM8489055 r1,GSM8489055,1,RNA from whole animals was extracted using phenol/chloroform isoamyl alcohol extraction. Libraries were cloned using Illumina TruSeq® Stranded mRNA Library Prep 20020595.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP529442,,,2_Whole_Body_WT.fastq.gz,fastq,3402592950.0,45367906.0,GSM8489055 r1,0:75,A:818791467;C:821633995;G:811228427;T:950887532;N:51529,75,,,,818791467,821633995,811228427,950887532,51529,SRX25901725,SRS22493411,SRA1958985,Stowers Institute for Medical Research,Stowers Institute for Medical Research,1,0.9698,,0.11276,,0.68562,,0.49148,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2024-08-29,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
33662,SRR30476762,SRX25901724,SRS22493409,SRP529442,PRJNA1154244,ZNF574 is a Quality Control Factor for Defective Ribosome Biogenesis Intermediates [RNA Seq],GSE275992,Transcriptome Analysis,Eukaryotic ribosome assembly is an intricate process that involves four ribosomal RNAs  80 ribosomal proteins  and over 200 biogenesis factors that take part in numerous interdependent steps. The complexity and essentiality of this process creates opportunities for deleterious mutations to occur  accumulate  and impact downstream cellular processes. “Dead end” ribosome intermediates that result from biogenesis errors are rapidly degraded  affirming the existence of quality control pathways that monitor ribosome assembly. However  the factors that differentiate between on path and dead end intermediates are unknown. We engineered a system to perturb ribosome assembly in human cells and discovered that faulty ribosomes are degraded via the ubiquitin proteasome system. We identified ZNF574 as a key component of a novel quality control pathway  which we term the Ribosome Assembly Surveillance Pathway RASP. In an animal model  loss of ZNF574 leads to developmental defects  further emphasizing the importance of RASP in organismal health. Overall design: To identify differentially expressed genes following the loss of znf574  we in crossed znf574+/  animals. znf574 wild type znf574+/+ or +/  and znf574 mutant znf574 /  larvae were phenotypically identified seven dpf Whole animals were used for this experiment. We performed RNA Seq followed by differential expression analysis with DESeq2  comparing differentially expressed genes between ZNF574 mutant and wild type animals.,,pubmed:40328246,,Whole Body WT R1,GSM8489054,,tissue:whole larvae|cell line:whole larvae|cell type:all cell types|genotype:znf574+/+ or znf574+/ |treatment:N1|time:NA|geo loc name:missing|collection date:missing,Whole Body WT R1,Reads were de multiplexed using Illumina’s bcl2fastq v2.20. Reads were aligned to the zebrafish genome GRCz11/danRer11 using kallisto v0.46.0. DESeq2 Galaxy Version 2.11.40+galaxy2 was used for differential expression analysis Genes with a minimum two fold upregulation in znf574 /  larvae and an adjusted p value of less than 0.05 were selected for further analysis. Pathway analysis was performed using the Kyoto Encyclopedia of Genes and Genomes database KEGG www.genome.jp/kegg. Pathway enrichment analyses were performed by using the Database for Annotation  Visualization and Integrated Discovery DAVID Bioinformatics  https://david.ncifcrf.gov/tools.jsp. Assembly: GRCz11/danRer11 Supplementary files format and content: tab separated value file that includes the raw count for each sample,whole larvae,znf574+/  heterozygous animals were in crossed  and fertilized eggs were collected and maintained in a zebrafish incubator for 8 days. Water was exchanged daily. Seven dpf  znf574 mutant animals can be easily distinguished from wild type siblings.,RNA from whole animals was extracted using phenol/chloroform isoamyl alcohol extraction. Libraries were cloned using Illumina TruSeq® Stranded mRNA Library Prep 20020595.,Adult zebrafish were maintained on a 14 h light–10 h dark cycle and fed once daily with 3.5% body weight of Gemma Micro 500 Skretting USA. All genotypes were bred into the wild type AB background.  All procedures comply with all relevant ethical regulations and were approved by the Carnegie Institution Animal Care and Use Committee Protocol #162 and the animal ethics committee IACUC review board at the Stowers Institute for MedicalResearch Protocol #2024 171.,cell line:whole larvae|cell type:all cell types|genotype:znf574+/+ or znf574+/ |treatment:N1|time:NA,GSM8489054,GSM8489054: Whole Body WT R1; Danio rerio; RNA Seq,GSM8489054 r1,GSM8489054,1,RNA from whole animals was extracted using phenol/chloroform isoamyl alcohol extraction. Libraries were cloned using Illumina TruSeq® Stranded mRNA Library Prep 20020595.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP529442,,,1_whole_body_wt.fastq.gz,fastq,3205662375.0,42742165.0,GSM8489054 r1,0:75,A:779998842;C:749239092;G:771273559;T:905099481;N:51401,75,,,,779998842,749239092,771273559,905099481,51401,SRX25901724,SRS22493409,SRA1958985,Stowers Institute for Medical Research,Stowers Institute for Medical Research,1,0.96846,,0.09359,,0.67239,,0.47109,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2024-08-29,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
35892,SRR33167519,SRX28428333,SRS24751206,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 AC7 S7,GSM8919392,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing,GRC355 AC7 S7,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2,GSM8919392,GSM8919392: GRC355 AC7 S7; Danio rerio; RNA Seq,GSM8919392 r1,GSM8919392,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_AC7_S7_R1_001.fastq.gz,fastq,2227335150.0,29697802.0,GSM8919392 r1,0:75,A:600851630;C:506204586;G:559397063;T:560849750;N:32121,75,,,,600851630,506204586,559397063,560849750,32121,SRX28428333,SRS24751206,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Multi-stage,Multi-stage,Multi-tissue,Multi-system
35893,SRR33167520,SRX28428332,SRS24751204,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 AC6 S11,GSM8919391,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing,GRC355 AC6 S11,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2,GSM8919391,GSM8919391: GRC355 AC6 S11; Danio rerio; RNA Seq,GSM8919391 r1,GSM8919391,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_AC6_S11_R1_001.fastq.gz,fastq,2585681925.0,34475759.0,GSM8919391 r1,0:75,A:689801171;C:608098568;G:666027069;T:621732490;N:22627,75,,,,689801171,608098568,666027069,621732490,22627,SRX28428332,SRS24751204,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Multi-stage,Multi-stage,Multi-tissue,Multi-system
35894,SRR33167521,SRX28428331,SRS24751205,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 AC5 S14,GSM8919390,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing,GRC355 AC5 S14,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2,GSM8919390,GSM8919390: GRC355 AC5 S14; Danio rerio; RNA Seq,GSM8919390 r1,GSM8919390,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_AC5_S14_R1_001.fastq.gz,fastq,2494451250.0,33259350.0,GSM8919390 r1,0:75,A:663836714;C:570411156;G:619148577;T:641019188;N:35615,75,,,,663836714,570411156,619148577,641019188,35615,SRX28428331,SRS24751205,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Multi-stage,Multi-stage,Multi-tissue,Multi-system
35895,SRR33167522,SRX28428330,SRS24751203,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 AC4 S16,GSM8919389,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing,GRC355 AC4 S16,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2,GSM8919389,GSM8919389: GRC355 AC4 S16; Danio rerio; RNA Seq,GSM8919389 r1,GSM8919389,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_AC4_S16_R1_001.fastq.gz,fastq,2318944500.0,30919260.0,GSM8919389 r1,0:75,A:622730628;C:558676778;G:600421168;T:537095873;N:20053,75,,,,622730628,558676778,600421168,537095873,20053,SRX28428330,SRS24751203,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Multi-stage,Multi-stage,Multi-tissue,Multi-system
35896,SRR33167523,SRX28428329,SRS24751201,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,GRC355 AC3 S10,GSM8919388,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2|geo loc name:missing|collection date:missing,GRC355 AC3 S10,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:2,GSM8919388,GSM8919388: GRC355 AC3 S10; Danio rerio; RNA Seq,GSM8919388 r1,GSM8919388,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP579141,,,GRC355_AC3_S10_R1_001.fastq.gz,fastq,2294756475.0,30596753.0,GSM8919388 r1,0:75,A:602530943;C:536584842;G:585162453;T:570445286;N:32951,75,,,,602530943,536584842,585162453,570445286,32951,SRX28428329,SRS24751201,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Multi-stage,Multi-stage,Multi-tissue,Multi-system