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"SRX21533024", "SRS18745490", "SRP457576", "PRJNA1010780", "Effect of egr3 knockout on gene expression of dissected zebrafish hearts", "GSE241935", "Transcriptome Analysis", "To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype  we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf.  We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS.  Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u00b5l of RNase free water.   Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples.   1. Boezio  G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571", null, "pubmed:38748804", null, "egr3 wild type siblings 2", "GSM7745909", null, "source name:Heart|tissue:Heart|genotype:bns577+/+|geo loc name:missing|collection date:missing", "egr3 wild type siblings 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al.  Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. 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Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype  we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf.  We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS.  Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u00b5l of RNase free water.   Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples.   1. Boezio  G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571", null, "pubmed:38748804", null, "egr3 wild type siblings 1", "GSM7745908", null, "source name:Heart|tissue:Heart|genotype:bns577+/+|geo loc name:missing|collection date:missing", "egr3 wild type siblings 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al.  Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. 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Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype  we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf.  We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS.  Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u00b5l of RNase free water.   Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples.   1. Boezio  G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571", null, "pubmed:38748804", null, "egr3 mutants 2", "GSM7745907", null, "source name:Heart|tissue:Heart|genotype:bns577 / |geo loc name:missing|collection date:missing", "egr3 mutants 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al.  Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts", "Heart", null, "Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "tissue:Heart|genotype:bns577 / ", "GSM7745907", "GSM7745907: egr3 mutants 2; Danio rerio; RNA Seq", "GSM7745907 r1", "GSM7745907", "1", "Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP457576", null, "loader:fastq load.py", "E22_3626_Lib_Agatha_egr3_Mut2_R1.fastq.gz", "fastq", 3432675258.0, 48483287.0, "GSM7745907 r1", "0:70.80", "A:925832958;C:788551205;G:790129536;T:927993012;N:168547", 70, null, null, null, 925832958, 788551205, 790129536, 927993012, 168547, "SRX21533022", "SRS18745488", "SRA1702458", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.75652, null, 0.04046, null, 0.76455, null, 0.46333, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-08-30", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [25323, "SRR25810881", "SRX21533021", "SRS18745487", "SRP457576", "PRJNA1010780", "Effect of egr3 knockout on gene expression of dissected zebrafish hearts", "GSE241935", "Transcriptome Analysis", "To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype  we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf.  We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS.  Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u00b5l of RNase free water.   Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples.   1. Boezio  G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571", null, "pubmed:38748804", null, "egr3 mutants 1", "GSM7745906", null, "source name:Heart|tissue:Heart|genotype:bns577 / |geo loc name:missing|collection date:missing", "egr3 mutants 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al.  Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts", "Heart", null, "Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "tissue:Heart|genotype:bns577 / ", "GSM7745906", "GSM7745906: egr3 mutants 1; Danio rerio; RNA Seq", "GSM7745906 r1", "GSM7745906", "1", "Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP457576", null, "loader:fastq load.py", "E22_3626_Lib_Agatha_egr3_Mut1_R1.fastq.gz", "fastq", 3838969347.0, 54545950.0, "GSM7745906 r1", "0:70.38", "A:1016913415;C:902500250;G:903033204;T:1016194618;N:327860", 70, null, null, null, 1016913415, 902500250, 903033204, 1016194618, 327860, "SRX21533021", "SRS18745487", "SRA1702458", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.9511, null, 0.05017, null, 0.75341, null, 0.47152, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-08-30", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [28470, "SRR26253203", "SRX21963295", "SRS19039869", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. 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However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.", null, null, null, null, "Small RNA IFN4 1", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 21|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA IFND1", "Small RNA IFND1", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "IFN4-1.deadaptor.fq.gz", "fastq", 289362334.0, 11048590.0, "IFN4 1.deadaptor.fq.gz", "0:26.19", "A:73933649;C:59386039;G:76847534;T:79184583;N:10529", 26, null, null, null, 73933649, 59386039, 76847534, 79184583, 10529, "SRX21963294", "SRS19039868", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.91683, null, 0.07099, null, 0.96132, null, 0.64882, null, 25, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28472, "SRR26253205", "SRX21963293", "SRS19039867", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.", null, null, null, null, "Small RNA IFN1 4", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 20|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA IFNA4", "Small RNA IFNA4", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "IFN1-4.deadaptor.fq.gz", "fastq", 270529395.0, 11070360.0, "IFN1 4.deadaptor.fq.gz", "0:24.44", "A:69759888;C:54924667;G:71358091;T:74470720;N:16029", 24, null, null, null, 69759888, 54924667, 71358091, 74470720, 16029, "SRX21963293", "SRS19039867", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.88469, null, 0.06696, null, 0.96664, null, 0.74853, null, 22, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28473, "SRR26253206", "SRX21963292", "SRS19039866", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.", null, null, null, null, "Small RNA IFN1 3", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 19|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA IFNA3", "Small RNA IFNA3", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "IFN1-3.deadaptor.fq.gz", "fastq", 353291957.0, 11740560.0, "IFN1 3.deadaptor.fq.gz", "0:30.09", "A:89026549;C:76490337;G:94719420;T:93036955;N:18696", 30, null, null, null, 89026549, 76490337, 94719420, 93036955, 18696, "SRX21963292", "SRS19039866", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.83151, null, 0.07199, null, 0.96471, null, 0.71641, null, 22, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28474, "SRR26253207", "SRX21963291", "SRS19039865", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.", null, null, null, null, "Small RNA IFN1 2", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 18|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA IFNA2", "Small RNA IFNA2", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "IFN1-2.deadaptor.fq.gz", "fastq", 257949577.0, 11213774.0, "IFN1 2.deadaptor.fq.gz", "0:23.00", "A:67371681;C:51128621;G:67605590;T:71826657;N:17028", 23, null, null, null, 67371681, 51128621, 67605590, 71826657, 17028, "SRX21963291", "SRS19039865", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.91396, null, 0.06536, null, 0.97197, null, 0.76269, null, 23, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28475, "SRR26253208", "SRX21963290", "SRS19039864", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.", null, null, null, null, "Small RNA IFN1 1", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 17|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA IFNA1", "Small RNA IFNA1", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "IFN1-1.deadaptor.fq.gz", "fastq", 329358383.0, 11799176.0, "IFN1 1.deadaptor.fq.gz", "0:27.91", "A:84093681;C:68961271;G:86502739;T:89779605;N:21087", 27, null, null, null, 84093681, 68961271, 86502739, 89779605, 21087, "SRX21963290", "SRS19039864", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.92116, null, 0.07483, null, 0.96796, null, 0.75179, null, 22, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28476, "SRR26253209", "SRX21963289", "SRS19039863", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.", null, null, null, null, "Small RNA Control 4", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 16|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA C4", "Small RNA C4", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "Control-4.deadaptor.fq.gz", "fastq", 251577736.0, 10951659.0, "Control 4.deadaptor.fq.gz", "0:22.97", "A:65382449;C:50041232;G:66038625;T:70106464;N:8966", 22, null, null, null, 65382449, 50041232, 66038625, 70106464, 8966, "SRX21963289", "SRS19039863", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.89744, null, 0.06821, null, 0.96607, null, 0.63829, null, 22, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28477, "SRR26253210", "SRX21963288", "SRS19039862", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.", null, null, null, null, "Small RNA Control 3", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 15|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA C3", "Small RNA C3", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "Control-3.deadaptor.fq.gz", "fastq", 252164979.0, 11004167.0, "Control 3.deadaptor.fq.gz", "0:22.92", "A:65850899;C:48466665;G:66708038;T:71130786;N:8591", 22, null, null, null, 65850899, 48466665, 66708038, 71130786, 8591, "SRX21963288", "SRS19039862", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.91567, null, 0.06804, null, 0.96278, null, 0.75579, null, 22, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28478, "SRR26253211", "SRX21963287", "SRS19039861", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.", null, null, null, null, "Small RNA IFN4 4", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 24|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA IFND4", "Small RNA IFND4", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "IFN4-4.deadaptor.fq.gz", "fastq", 291708053.0, 11503883.0, "IFN4 4.deadaptor.fq.gz", "0:25.36", "A:74079231;C:61368459;G:76898572;T:79351225;N:10566", 25, null, null, null, 74079231, 61368459, 76898572, 79351225, 10566, "SRX21963287", "SRS19039861", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.88888, null, 0.0633, null, 0.97305, null, 0.74862, null, 23, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28479, "SRR26253212", "SRX21963286", "SRS19039860", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.", null, null, null, null, "Small RNA IFN4 3", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 23|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA IFND3", "Small RNA IFND3", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "IFN4-3.deadaptor.fq.gz", "fastq", 349995495.0, 11885662.0, "IFN4 3.deadaptor.fq.gz", "0:29.45", "A:87443709;C:76373108;G:92741296;T:93425866;N:11516", 29, null, null, null, 87443709, 76373108, 92741296, 93425866, 11516, "SRX21963286", "SRS19039860", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.92619, null, 0.06843, null, 0.9709, null, 0.74977, null, 73, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28480, "SRR26253213", "SRX21963285", "SRS19039859", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.", null, null, null, null, "Small RNA Control 2", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 14|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA C2", "Small RNA C2", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "Control-2.deadaptor.fq.gz", "fastq", 254163676.0, 10744164.0, "Control 2.deadaptor.fq.gz", "0:23.66", "A:66003417;C:49309846;G:67463940;T:71377644;N:8829", 23, null, null, null, 66003417, 49309846, 67463940, 71377644, 8829, "SRX21963285", "SRS19039859", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.93068, null, 0.06626, null, 0.96441, null, 0.7492, null, 22, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28481, "SRR26253214", "SRX21963284", "SRS19039858", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.", null, null, null, null, "Small RNA Control 1", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 13|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA C1", "Small RNA C1", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "Control-1.deadaptor.fq.gz", "fastq", 267090429.0, 11027241.0, "Control 1.deadaptor.fq.gz", "0:24.22", "A:70162511;C:50705437;G:69872659;T:76339682;N:10140", 24, null, null, null, 70162511, 50705437, 69872659, 76339682, 10140, "SRX21963284", "SRS19039858", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.93267, null, 0.07189, null, 0.96735, null, 0.75447, null, 21, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [31502, "SRR28411462", "SRX24015869", "SRS20810998", "SRP497025", "PRJNA1090509", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139", "GSE262169", "Transcriptome Analysis", "The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing", "parent bioproject:PRJNA1090894", "pubmed:39271818", null, "injured tissue  myd88+/+  24 hpci 2", "GSM8159071", null, "source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "injured tissue  myd88+/+  24 hpci 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts", "cardiac ventricles", "untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture\u2019s protocol Vazyme.", null, "tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment:cardiac cryoinjury", "GSM8159071", "GSM8159071: injured tissue  myd88+/+  24 hpci 2; Danio rerio; RNA Seq", "GSM8159071 r1", "GSM8159071", "1", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "loader:fastq load.py", "Pinelopi_WT2_24h_pci_R1.fastq.gz", "fastq", 2454645976.0, 33159360.0, "GSM8159071 r1", "0:74.03", "A:660213492;C:527347733;G:572126573;T:694765347;N:192831", 74, null, null, null, 660213492, 527347733, 572126573, 694765347, 192831, "SRX24015869", "SRS20810998", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2024-03-21", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31503, "SRR28411463", "SRX24015868", "SRS20810997", "SRP497025", "PRJNA1090509", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139", "GSE262169", "Transcriptome Analysis", "The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing", "parent bioproject:PRJNA1090894", "pubmed:39271818", null, "injured tissue  myd88+/+  1 hpci 2", "GSM8159070", null, "source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "injured tissue  myd88+/+  1 hpci 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts", "cardiac ventricles", "untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture\u2019s protocol Vazyme.", null, "tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment:cardiac cryoinjury", "GSM8159070", "GSM8159070: injured tissue  myd88+/+  1 hpci 2; Danio rerio; RNA Seq", "GSM8159070 r1", "GSM8159070", "1", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "loader:fastq load.py", "Pinelopi_WT2_1h_pci_R1.fastq.gz", "fastq", 2674654542.0, 36003719.0, "GSM8159070 r1", "0:74.29", "A:713621237;C:556223861;G:630990745;T:773686189;N:132510", 74, null, null, null, 713621237, 556223861, 630990745, 773686189, 132510, "SRX24015868", "SRS20810997", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2024-03-21", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31504, "SRR28411464", "SRX24015867", "SRS20810996", "SRP497025", "PRJNA1090509", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139", "GSE262169", "Transcriptome Analysis", "The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing", "parent bioproject:PRJNA1090894", "pubmed:39271818", null, "ventricle  myd88+/+  untouched 2", "GSM8159069", null, "source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment: |geo loc name:missing|collection date:missing", "ventricle  myd88+/+  untouched 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts", "cardiac ventricles", "untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture\u2019s protocol Vazyme.", null, "tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment: ", "GSM8159069", "GSM8159069: ventricle  myd88+/+  untouched 2; Danio rerio; RNA Seq", "GSM8159069 r1", "GSM8159069", "1", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "loader:fastq load.py", "Pinelopi_WT2_0h_pci_R1.fastq.gz", "fastq", 2092632406.0, 28163739.0, "GSM8159069 r1", "0:74.30", "A:560190602;C:446185315;G:485011548;T:601082958;N:161983", 74, null, null, null, 560190602, 446185315, 485011548, 601082958, 161983, "SRX24015867", "SRS20810996", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2024-03-21", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31505, "SRR28411465", "SRX24015866", "SRS20810995", "SRP497025", "PRJNA1090509", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139", "GSE262169", "Transcriptome Analysis", "The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing", "parent bioproject:PRJNA1090894", "pubmed:39271818", null, "injured tissue  myd88+/+  24 hpci 1", "GSM8159068", null, "source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "injured tissue  myd88+/+  24 hpci 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts", "cardiac ventricles", "untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture\u2019s protocol Vazyme.", null, "tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment:cardiac cryoinjury", "GSM8159068", "GSM8159068: injured tissue  myd88+/+  24 hpci 1; Danio rerio; RNA Seq", "GSM8159068 r1", "GSM8159068", "1", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "loader:fastq load.py", "Pinelopi_WT1_24h_pci_R1.fastq.gz", "fastq", 1060148110.0, 14341826.0, "GSM8159068 r1", "0:73.92", "A:290655996;C:222128471;G:247491826;T:299784598;N:87219", 73, null, null, null, 290655996, 222128471, 247491826, 299784598, 87219, "SRX24015866", "SRS20810995", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2024-03-21", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31506, "SRR28411466", "SRX24015865", "SRS20810994", "SRP497025", "PRJNA1090509", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139", "GSE262169", "Transcriptome Analysis", "The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing", "parent bioproject:PRJNA1090894", "pubmed:39271818", null, "injured tissue  myd88+/+  1 hpci 1", "GSM8159067", null, "source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "injured tissue  myd88+/+  1 hpci 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts", "cardiac ventricles", "untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture\u2019s protocol Vazyme.", null, "tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment:cardiac cryoinjury", "GSM8159067", "GSM8159067: injured tissue  myd88+/+  1 hpci 1; Danio rerio; RNA Seq", "GSM8159067 r1", "GSM8159067", "1", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "loader:fastq load.py", "Pinelopi_WT1_1h_pci_R1.fastq.gz", "fastq", 2594786024.0, 34913792.0, "GSM8159067 r1", "0:74.32", "A:689702458;C:551265040;G:603307580;T:750425733;N:85213", 74, null, null, null, 689702458, 551265040, 603307580, 750425733, 85213, "SRX24015865", "SRS20810994", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2024-03-21", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31507, "SRR28411467", "SRX24015864", "SRS20810993", "SRP497025", "PRJNA1090509", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139", "GSE262169", "Transcriptome Analysis", "The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing", "parent bioproject:PRJNA1090894", "pubmed:39271818", null, "ventricle  myd88+/+  untouched 1", "GSM8159066", null, "source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment: |geo loc name:missing|collection date:missing", "ventricle  myd88+/+  untouched 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts", "cardiac ventricles", "untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture\u2019s protocol Vazyme.", null, "tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88+/+|treatment: ", "GSM8159066", "GSM8159066: ventricle  myd88+/+  untouched 1; Danio rerio; RNA Seq", "GSM8159066 r1", "GSM8159066", "1", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "loader:fastq load.py", "Pinelopi_WT1_0h_pci_R1.fastq.gz", "fastq", 2123516005.0, 28595227.0, "GSM8159066 r1", "0:74.26", "A:562046544;C:458761205;G:496224794;T:606313940;N:169522", 74, null, null, null, 562046544, 458761205, 496224794, 606313940, 169522, "SRX24015864", "SRS20810993", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2024-03-21", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31508, "SRR28411468", "SRX24015863", "SRS20810992", "SRP497025", "PRJNA1090509", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139", "GSE262169", "Transcriptome Analysis", "The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing", "parent bioproject:PRJNA1090894", "pubmed:39271818", null, "injured tissue  myd88 /   24 hpci 2", "GSM8159065", null, "source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "injured tissue  myd88 /   24 hpci 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts", "cardiac ventricles", "untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture\u2019s protocol Vazyme.", null, "tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury", "GSM8159065", "GSM8159065: injured tissue  myd88 /   24 hpci 2; Danio rerio; RNA Seq", "GSM8159065 r1", "GSM8159065", "1", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "loader:fastq load.py", "Pinelopi_Homo2_24h_pci_R1.fastq.gz", "fastq", 2509143345.0, 33915175.0, "GSM8159065 r1", "0:73.98", "A:669128241;C:547606289;G:587771598;T:704439682;N:197535", 73, null, null, null, 669128241, 547606289, 587771598, 704439682, 197535, "SRX24015863", "SRS20810992", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2024-03-21", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31509, "SRR28411469", "SRX24015862", "SRS20810991", "SRP497025", "PRJNA1090509", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139", "GSE262169", "Transcriptome Analysis", "The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing", "parent bioproject:PRJNA1090894", "pubmed:39271818", null, "injured tissue  myd88 /   1 hpci 2", "GSM8159064", null, "source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "injured tissue  myd88 /   1 hpci 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts", "cardiac ventricles", "untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture\u2019s protocol Vazyme.", null, "tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury", "GSM8159064", "GSM8159064: injured tissue  myd88 /   1 hpci 2; Danio rerio; RNA Seq", "GSM8159064 r1", "GSM8159064", "1", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "loader:fastq load.py", "Pinelopi_Homo2_1h_pci_R1.fastq.gz", "fastq", 2584847185.0, 34784917.0, "GSM8159064 r1", "0:74.31", "A:690941775;C:542509296;G:605002938;T:746301098;N:92078", 74, null, null, null, 690941775, 542509296, 605002938, 746301098, 92078, "SRX24015862", "SRS20810991", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2024-03-21", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31510, "SRR28411470", "SRX24015861", "SRS20810990", "SRP497025", "PRJNA1090509", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139", "GSE262169", "Transcriptome Analysis", "The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing", "parent bioproject:PRJNA1090894", "pubmed:39271818", null, "ventricle  myd88 /   untouched 2", "GSM8159063", null, "source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment: |geo loc name:missing|collection date:missing", "ventricle  myd88 /   untouched 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts", "cardiac ventricles", "untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture\u2019s protocol Vazyme.", null, "tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment: ", "GSM8159063", "GSM8159063: ventricle  myd88 /   untouched 2; Danio rerio; RNA Seq", "GSM8159063 r1", "GSM8159063", "1", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "loader:fastq load.py", "Pinelopi_Homo2_0h_pci_R1.fastq.gz", "fastq", 2178164776.0, 29313471.0, "GSM8159063 r1", "0:74.31", "A:588370831;C:457110464;G:507924919;T:624586577;N:171985", 74, null, null, null, 588370831, 457110464, 507924919, 624586577, 171985, "SRX24015861", "SRS20810990", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2024-03-21", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31511, "SRR28411471", "SRX24015860", "SRS20810989", "SRP497025", "PRJNA1090509", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139", "GSE262169", "Transcriptome Analysis", "The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing", "parent bioproject:PRJNA1090894", "pubmed:39271818", null, "injured tissue  myd88 /   24 hpci 1", "GSM8159062", null, "source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "injured tissue  myd88 /   24 hpci 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts", "cardiac ventricles", "untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture\u2019s protocol Vazyme.", null, "tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury", "GSM8159062", "GSM8159062: injured tissue  myd88 /   24 hpci 1; Danio rerio; RNA Seq", "GSM8159062 r1", "GSM8159062", "1", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "loader:fastq load.py", "Pinelopi_Homo1_24h_pci_R1.fastq.gz", "fastq", 2323298254.0, 31332951.0, "GSM8159062 r1", "0:74.15", "A:621931320;C:501998000;G:541224122;T:657957821;N:186991", 74, null, null, null, 621931320, 501998000, 541224122, 657957821, 186991, "SRX24015860", "SRS20810989", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2024-03-21", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31512, "SRR28411472", "SRX24015859", "SRS20810988", "SRP497025", "PRJNA1090509", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139", "GSE262169", "Transcriptome Analysis", "The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing", "parent bioproject:PRJNA1090894", "pubmed:39271818", null, "injured tissue  myd88 /   1 hpci 1", "GSM8159061", null, "source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "injured tissue  myd88 /   1 hpci 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts", "cardiac ventricles", "untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture\u2019s protocol Vazyme.", null, "tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury", "GSM8159061", "GSM8159061: injured tissue  myd88 /   1 hpci 1; Danio rerio; RNA Seq", "GSM8159061 r1", "GSM8159061", "1", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "loader:fastq load.py", "Pinelopi_Homo1_1h_pci_R1.fastq.gz", "fastq", 2585736865.0, 34790236.0, "GSM8159061 r1", "0:74.32", "A:679380332;C:554919862;G:604907160;T:746451941;N:77570", 74, null, null, null, 679380332, 554919862, 604907160, 746451941, 77570, "SRX24015859", "SRS20810988", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2024-03-21", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31513, "SRR28411473", "SRX24015858", "SRS20810987", "SRP497025", "PRJNA1090509", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139", "GSE262169", "Transcriptome Analysis", "The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration  but many questions remain about its exact role.  Here we show that MyD88  a key component of the innate immune response  controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  We find in cryoinjured myd88 /  ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population.  Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium and increased myofibroblasts and scarring.  Notably  endothelial specific overexpression of myd88 reverses these neutrophil  fibrotic  and scarring phenotypes.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway  and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 /  untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing", "parent bioproject:PRJNA1090894", "pubmed:39271818", null, "ventricle  myd88 /   untouched 1", "GSM8159060", null, "source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment: |geo loc name:missing|collection date:missing", "ventricle  myd88 /   untouched 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts", "cardiac ventricles", "untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture\u2019s protocol Vazyme.", null, "tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment: ", "GSM8159060", "GSM8159060: ventricle  myd88 /   untouched 1; Danio rerio; RNA Seq", "GSM8159060 r1", "GSM8159060", "1", "RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set  Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP497025", null, "loader:fastq load.py", "Pinelopi_Homo1_0h_pci_R1.fastq.gz", "fastq", 2321007700.0, 31228476.0, "GSM8159060 r1", "0:74.32", "A:623574024;C:490503071;G:538918126;T:667825381;N:187098", 74, null, null, null, 623574024, 490503071, 538918126, 667825381, 187098, "SRX24015858", "SRS20810987", "SRA1830778", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2024-03-21", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31896, "SRR28745432", "SRX24311225", "SRS21073227", "SRP502845", "PRJNA1102356", "flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response", "GSE264406", "Transcriptome Analysis", "VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.", null, "pubmed:39612288", null, "wild type heart  96 hours post cryoinjury 3", "GSM8217704", null, "source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "wild type heart  96 hours post cryoinjury 3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix", "heart ventricle border zone and injured area", null, "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury", "GSM8217704", "GSM8217704: wild type heart  96 hours post cryoinjury 3; Danio rerio; RNA Seq", "GSM8217704 r1", "GSM8217704", "1", "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "loader:fastq load.py", "E23_4173_Armaad_Lib_WT3_R1.fastq.gz", "fastq", 3257983192.0, 47556048.0, "GSM8217704 r1", "0:68.51", "A:848972796;C:741588101;G:760680137;T:905607069;N:1135089", 68, null, null, null, 848972796, 741588101, 760680137, 905607069, 1135089, "SRX24311225", "SRS21073227", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94185, null, 0.087, null, 0.72478, null, 0.50388, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31897, "SRR28745433", "SRX24311224", "SRS21073229", "SRP502845", "PRJNA1102356", "flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response", "GSE264406", "Transcriptome Analysis", "VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.", null, "pubmed:39612288", null, "wild type heart  96 hours post cryoinjury 2", "GSM8217703", null, "source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "wild type heart  96 hours post cryoinjury 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix", "heart ventricle border zone and injured area", null, "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury", "GSM8217703", "GSM8217703: wild type heart  96 hours post cryoinjury 2; Danio rerio; RNA Seq", "GSM8217703 r1", "GSM8217703", "1", "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "loader:fastq load.py", "E23_4173_Armaad_Lib_WT2_R1.fastq.gz", "fastq", 3864619254.0, 56519751.0, "GSM8217703 r1", "0:68.38", "A:1003402543;C:880721584;G:903469106;T:1075304136;N:1721885", 68, null, null, null, 1003402543, 880721584, 903469106, 1075304136, 1721885, "SRX24311224", "SRS21073229", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.93928, null, 0.08915, null, 0.72348, null, 0.49993, null, 71, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31898, "SRR28745434", "SRX24311223", "SRS21073228", "SRP502845", "PRJNA1102356", "flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response", "GSE264406", "Transcriptome Analysis", "VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.", null, "pubmed:39612288", null, "wild type heart  96 hours post cryoinjury 1", "GSM8217702", null, "source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "wild type heart  96 hours post cryoinjury 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix", "heart ventricle border zone and injured area", null, "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury", "GSM8217702", "GSM8217702: wild type heart  96 hours post cryoinjury 1; Danio rerio; RNA Seq", "GSM8217702 r1", "GSM8217702", "1", "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "loader:fastq load.py", "E23_4173_Armaad_Lib_WT1_R1.fastq.gz", "fastq", 3571478400.0, 52133215.0, "GSM8217702 r1", "0:68.51", "A:928171678;C:814216251;G:835024543;T:992630615;N:1435313", 68, null, null, null, 928171678, 814216251, 835024543, 992630615, 1435313, "SRX24311223", "SRS21073228", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94111, null, 0.08647, null, 0.72922, null, 0.50812, null, 42, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31899, "SRR28745435", "SRX24311222", "SRS21073226", "SRP502845", "PRJNA1102356", "flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response", "GSE264406", "Transcriptome Analysis", "VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.", null, "pubmed:39612288", null, "flt1 mutant heart  96 hours post cryoinjury 3", "GSM8217701", null, "source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "flt1 mutant heart  96 hours post cryoinjury 3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix", "heart ventricle border zone and injured area", null, "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury", "GSM8217701", "GSM8217701: flt1 mutant heart  96 hours post cryoinjury 3; Danio rerio; RNA Seq", "GSM8217701 r1", "GSM8217701", "1", "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "loader:fastq load.py", "E23_4173_Armaad_Lib_FLT_MUT3_R1.fastq.gz", "fastq", 4085359270.0, 59673604.0, "GSM8217701 r1", "0:68.46", "A:1050667797;C:938174838;G:953989485;T:1140941596;N:1585554", 68, null, null, null, 1050667797, 938174838, 953989485, 1140941596, 1585554, "SRX24311222", "SRS21073226", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94035, null, 0.08631, null, 0.72376, null, 0.49828, null, 69, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31900, "SRR28745436", "SRX24311221", "SRS21073225", "SRP502845", "PRJNA1102356", "flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response", "GSE264406", "Transcriptome Analysis", "VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.", null, "pubmed:39612288", null, "flt1 mutant heart  96 hours post cryoinjury 2", "GSM8217700", null, "source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "flt1 mutant heart  96 hours post cryoinjury 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix", "heart ventricle border zone and injured area", null, "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury", "GSM8217700", "GSM8217700: flt1 mutant heart  96 hours post cryoinjury 2; Danio rerio; RNA Seq", "GSM8217700 r1", "GSM8217700", "1", "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "loader:fastq load.py", "E23_4173_Armaad_Lib_FLT_MUT2_R1.fastq.gz", "fastq", 4696922408.0, 68645737.0, "GSM8217700 r1", "0:68.42", "A:1220019708;C:1072448104;G:1106194472;T:1296618556;N:1641568", 68, null, null, null, 1220019708, 1072448104, 1106194472, 1296618556, 1641568, "SRX24311221", "SRS21073225", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94205, null, 0.08792, null, 0.72543, null, 0.50566, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31901, "SRR28745437", "SRX24311220", "SRS21073224", "SRP502845", "PRJNA1102356", "flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response", "GSE264406", "Transcriptome Analysis", "VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.", null, "pubmed:39612288", null, "flt1 mutant heart  96 hours post cryoinjury 1", "GSM8217699", null, "source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "flt1 mutant heart  96 hours post cryoinjury 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix", "heart ventricle border zone and injured area", null, "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury", "GSM8217699", "GSM8217699: flt1 mutant heart  96 hours post cryoinjury 1; Danio rerio; RNA Seq", "GSM8217699 r1", "GSM8217699", "1", "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "loader:fastq load.py", "E23_4173_Armaad_Lib_FLT_MUT1_R1.fastq.gz", "fastq", 2897934017.0, 42657803.0, "GSM8217699 r1", "0:67.93", "A:749045495;C:662930035;G:683478060;T:800853726;N:1626701", 67, null, null, null, 749045495, 662930035, 683478060, 800853726, 1626701, "SRX24311220", "SRS21073224", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94107, null, 0.08304, null, 0.72579, null, 0.50482, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31986, "SRR28894021", "SRX24452441", "SRS21206092", "SRP505663", "PRJNA1107798", "liver", "PRJNA1107798", "Other", "wt and elovl2 mutant liver", null, null, null, null, "elovl2 4", null, "strain:elovl2 4|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "elovl2 4", "8", "8", "liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "SRP505663", null, null, "elovl2-4", "fastq", 4367010000.0, 29113400.0, "elovl2 4.gz", "0:150", "A:1161921878;C:1015107709;G:1012841192;T:1177020487;N:118734", 150, null, null, null, 1161921878, 1015107709, 1012841192, 1177020487, 118734, "SRX24452441", "SRS21206092", "SRA1858809", "Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology", "Chinese Academy of Sciences (CAS)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-05-04", "Undetermined", "Undetermined", "Liver", "Liver and Biliary System"], [31987, "SRR28894022", "SRX24452440", "SRS21206091", "SRP505663", "PRJNA1107798", "liver", "PRJNA1107798", "Other", "wt and elovl2 mutant liver", null, null, null, null, "elovl2 3", null, "strain:elovl2 3|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "elovl2 3", "7", "7", "liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "SRP505663", null, null, "elovl2-3", "fastq", 5125533150.0, 34170221.0, "elovl2 3.gz", "0:150", "A:1365645170;C:1189846405;G:1184721703;T:1385180096;N:139776", 150, null, null, null, 1365645170, 1189846405, 1184721703, 1385180096, 139776, "SRX24452440", "SRS21206091", "SRA1858809", "Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology", "Chinese Academy of Sciences (CAS)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-05-04", "Undetermined", "Undetermined", "Liver", "Liver and Biliary System"], [31988, "SRR28894023", "SRX24452439", "SRS21206090", "SRP505663", "PRJNA1107798", "liver", "PRJNA1107798", "Other", "wt and elovl2 mutant liver", null, null, null, null, "elovl2 2", null, "strain:elovl2 2|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "elovl2 2", "6", "6", "liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "SRP505663", null, null, "elovl2-2", "fastq", 3261375750.0, 21742505.0, "elovl2 2.gz", "0:150", "A:878478836;C:747963062;G:743760185;T:891083235;N:90432", 150, null, null, null, 878478836, 747963062, 743760185, 891083235, 90432, "SRX24452439", "SRS21206090", "SRA1858809", "Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology", "Chinese Academy of Sciences (CAS)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-05-04", "Undetermined", "Undetermined", "Liver", "Liver and Biliary System"], [31989, "SRR28894024", "SRX24452438", "SRS21206089", "SRP505663", "PRJNA1107798", "liver", "PRJNA1107798", "Other", "wt and elovl2 mutant liver", null, null, null, null, "elovl2 1", null, "strain:elovl2 1|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "elovl2 1", "5", "5", "liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "SRP505663", null, null, "elovl2-1", "fastq", 3629422950.0, 24196153.0, "elovl2 1.gz", "0:150", "A:974034477;C:836070594;G:831068189;T:988151010;N:98680", 150, null, null, null, 974034477, 836070594, 831068189, 988151010, 98680, "SRX24452438", "SRS21206089", "SRA1858809", "Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology", "Chinese Academy of Sciences (CAS)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-05-04", "Undetermined", "Undetermined", "Liver", "Liver and Biliary System"], [31990, "SRR28894025", "SRX24452437", "SRS21206088", "SRP505663", "PRJNA1107798", "liver", "PRJNA1107798", "Other", "wt and elovl2 mutant liver", null, null, null, null, "WT 4", null, "strain:WT 4|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "WT 4", "4", "4", "liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "SRP505663", null, null, "WT-4", "fastq", 4037472900.0, 26916486.0, "WT 4.gz", "0:150", "A:1083383010;C:932278459;G:925831402;T:1095868616;N:111413", 150, null, null, null, 1083383010, 932278459, 925831402, 1095868616, 111413, "SRX24452437", "SRS21206088", "SRA1858809", "Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology", "Chinese Academy of Sciences (CAS)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-05-04", "Undetermined", "Undetermined", "Liver", "Liver and Biliary System"], [31991, "SRR28894026", "SRX24452436", "SRS21206087", "SRP505663", "PRJNA1107798", "liver", "PRJNA1107798", "Other", "wt and elovl2 mutant liver", null, null, null, null, "WT 3", null, "strain:WT 3|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "WT 3", "3", "3", "liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "SRP505663", null, null, "WT-3", "fastq", 3651994200.0, 24346628.0, "WT 3.gz", "0:150", "A:978819903;C:844506880;G:836704943;T:991863415;N:99059", 150, null, null, null, 978819903, 844506880, 836704943, 991863415, 99059, "SRX24452436", "SRS21206087", "SRA1858809", "Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology", "Chinese Academy of Sciences (CAS)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-05-04", "Undetermined", "Undetermined", "Liver", "Liver and Biliary System"], [31992, "SRR28894027", "SRX24452435", "SRS21206086", "SRP505663", "PRJNA1107798", "liver", "PRJNA1107798", "Other", "wt and elovl2 mutant liver", null, null, null, null, "WT 2", null, "strain:WT 2|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "WT 2", "2", "2", "liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "SRP505663", null, null, "WT-2", "fastq", 3845338950.0, 25635593.0, "WT 2.gz", "0:150", "A:1033991995;C:885977441;G:878907105;T:1046356459;N:105950", 150, null, null, null, 1033991995, 885977441, 878907105, 1046356459, 105950, "SRX24452435", "SRS21206086", "SRA1858809", "Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology", "Chinese Academy of Sciences (CAS)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-05-04", "Undetermined", "Undetermined", "Liver", "Liver and Biliary System"], [31993, "SRR28894028", "SRX24452434", "SRS21206085", "SRP505663", "PRJNA1107798", "liver", "PRJNA1107798", "Other", "wt and elovl2 mutant liver", null, null, null, null, "WT 1", null, "strain:WT 1|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "WT 1", "1", "1", "liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "SRP505663", null, null, "WT-1", "fastq", 3756883050.0, 25045887.0, "WT 1.gz", "0:150", "A:1005244721;C:868304979;G:865360007;T:1017811504;N:161839", 150, null, null, null, 1005244721, 868304979, 865360007, 1017811504, 161839, "SRX24452434", "SRS21206085", "SRA1858809", "Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology", "Chinese Academy of Sciences (CAS)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-05-04", "Undetermined", "Undetermined", "Liver", "Liver and Biliary System"], [33296, "SRR29925297", "SRX25419305", "SRS22079478", "SRP521541", "PRJNA1139080", "Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER Phagy", "GSE272836", "Transcriptome Analysis", "RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However  the regulatory mechanisms connecting these processes remain poorly understood. Here  we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic five prime splice sites. Importantly  disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. These spurious isoforms disrupt proteostasis causing cytosolic protein aggregates and ER stress. Proteotoxic exons activate unfolded protein response  causing CHOP mediated cell death. In response to impaired splicing  eukaryotic cells enhance ubiquitination and ER phagy to alleviate the pathogenic accumulation of proteotoxic isoforms. Our findings show how cryptic splicing induced proteotoxicity can be mitigated  and provide insight into the molecular pathogenesis of spliceosome associated diseases such as retinitis pigmentosa. Overall design: Comparative gene expression profiling analysis of RNA seq data for WT Zebrafish and its morpholino usp39 KD derivarive", null, "pubmed:39541449", null, "Zebrafish  usp39  4", "GSM8413284", null, "source name:whole organism|tissue:whole organism|strain:AB line|genotype:ups39 CRISPR/Cas9 KO|geo loc name:missing|collection date:missing", "Zebrafish  usp39  4", "BCL convert  v4.0.3 Sequence reads were trimmed for adaptor sequences/low quality sequences using Trimmomatic  v0.40 rc1  parameters ILLUMINACLIP: TruSeq3 SE.fa:2:30:10; CROP:111; HEADCROP:12 GENCODE annotation was used to map reads to the zebrafish genome version Danio rerio.GRCz11.110 with STAR  v2.7.11a  parameters:   runMode alignReads:   outSAMtype BAM SortedByCoordinate; Count reads into exons was determined by using the htseq count  v1.99.2 Differential gene expression analysis was done with DESeq2  v1.42.1 Assembly: Danio rerio.GRCz11.110 Supplementary files format and content: tab delminted text file includes raw count for each Sample", "whole organism", null, "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer\u2019s instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer\u2019s instructions.", null, "tissue:whole organism|strain:AB line|genotype:ups39 CRISPR/Cas9 KO", "GSM8413284", "GSM8413284: Zebrafish  usp39  4; Danio rerio; RNA Seq", "GSM8413284 r1", "GSM8413284", "1", "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer's instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP521541", null, null, "usp39_4_S8_R1_001.fastq.gz", "fastq", 6295309328.0, 56208119.0, "GSM8413284 r1", "0:112", "A:1916741141;C:1289239611;G:1409536874;T:1678402242;N:1389460", 112, null, null, null, 1916741141, 1289239611, 1409536874, 1678402242, 1389460, "SRX25419305", "SRS22079478", "SRA1930695", "Institute of Biochemistry II", "Institute of Biochemistry II", 1, 0.612, null, 0.25838, null, 0.70928, null, 0.47251, null, 112, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "rrna_depletion", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2024-07-23", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [33297, "SRR29925294", "SRX25419304", "SRS22079477", "SRP521541", "PRJNA1139080", "Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER Phagy", "GSE272836", "Transcriptome Analysis", "RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However  the regulatory mechanisms connecting these processes remain poorly understood. Here  we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic five prime splice sites. Importantly  disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. These spurious isoforms disrupt proteostasis causing cytosolic protein aggregates and ER stress. Proteotoxic exons activate unfolded protein response  causing CHOP mediated cell death. In response to impaired splicing  eukaryotic cells enhance ubiquitination and ER phagy to alleviate the pathogenic accumulation of proteotoxic isoforms. Our findings show how cryptic splicing induced proteotoxicity can be mitigated  and provide insight into the molecular pathogenesis of spliceosome associated diseases such as retinitis pigmentosa. Overall design: Comparative gene expression profiling analysis of RNA seq data for WT Zebrafish and its morpholino usp39 KD derivarive", null, "pubmed:39541449", null, "Zebrafish  usp39  3", "GSM8413283", null, "source name:whole organism|tissue:whole organism|strain:AB line|genotype:ups39 CRISPR/Cas9 KO|geo loc name:missing|collection date:missing", "Zebrafish  usp39  3", "BCL convert  v4.0.3 Sequence reads were trimmed for adaptor sequences/low quality sequences using Trimmomatic  v0.40 rc1  parameters ILLUMINACLIP: TruSeq3 SE.fa:2:30:10; CROP:111; HEADCROP:12 GENCODE annotation was used to map reads to the zebrafish genome version Danio rerio.GRCz11.110 with STAR  v2.7.11a  parameters:   runMode alignReads:   outSAMtype BAM SortedByCoordinate; Count reads into exons was determined by using the htseq count  v1.99.2 Differential gene expression analysis was done with DESeq2  v1.42.1 Assembly: Danio rerio.GRCz11.110 Supplementary files format and content: tab delminted text file includes raw count for each Sample", "whole organism", null, "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer\u2019s instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer\u2019s instructions.", null, "tissue:whole organism|strain:AB line|genotype:ups39 CRISPR/Cas9 KO", "GSM8413283", "GSM8413283: Zebrafish  usp39  3; Danio rerio; RNA Seq", "GSM8413283 r1", "GSM8413283", "1", "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer's instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP521541", null, null, "usp39_3_S7_R1_001.fastq.gz", "fastq", 4746730912.0, 42381526.0, "GSM8413283 r1", "0:112", "A:1404624435;C:989965185;G:1138331976;T:1212764925;N:1044391", 112, null, null, null, 1404624435, 989965185, 1138331976, 1212764925, 1044391, "SRX25419304", "SRS22079477", "SRA1930695", "Institute of Biochemistry II", "Institute of Biochemistry II", 1, 0.58824, null, 0.22238, null, 0.71181, null, 0.46377, null, 112, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "rrna_depletion", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2024-07-23", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [33298, "SRR29925295", "SRX25419303", "SRS22079474", "SRP521541", "PRJNA1139080", "Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER Phagy", "GSE272836", "Transcriptome Analysis", "RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However  the regulatory mechanisms connecting these processes remain poorly understood. Here  we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic five prime splice sites. Importantly  disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. These spurious isoforms disrupt proteostasis causing cytosolic protein aggregates and ER stress. Proteotoxic exons activate unfolded protein response  causing CHOP mediated cell death. In response to impaired splicing  eukaryotic cells enhance ubiquitination and ER phagy to alleviate the pathogenic accumulation of proteotoxic isoforms. Our findings show how cryptic splicing induced proteotoxicity can be mitigated  and provide insight into the molecular pathogenesis of spliceosome associated diseases such as retinitis pigmentosa. Overall design: Comparative gene expression profiling analysis of RNA seq data for WT Zebrafish and its morpholino usp39 KD derivarive", null, "pubmed:39541449", null, "Zebrafish  usp39  2", "GSM8413282", null, "source name:whole organism|tissue:whole organism|strain:AB line|genotype:ups39 CRISPR/Cas9 KO|geo loc name:missing|collection date:missing", "Zebrafish  usp39  2", "BCL convert  v4.0.3 Sequence reads were trimmed for adaptor sequences/low quality sequences using Trimmomatic  v0.40 rc1  parameters ILLUMINACLIP: TruSeq3 SE.fa:2:30:10; CROP:111; HEADCROP:12 GENCODE annotation was used to map reads to the zebrafish genome version Danio rerio.GRCz11.110 with STAR  v2.7.11a  parameters:   runMode alignReads:   outSAMtype BAM SortedByCoordinate; Count reads into exons was determined by using the htseq count  v1.99.2 Differential gene expression analysis was done with DESeq2  v1.42.1 Assembly: Danio rerio.GRCz11.110 Supplementary files format and content: tab delminted text file includes raw count for each Sample", "whole organism", null, "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer\u2019s instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer\u2019s instructions.", null, "tissue:whole organism|strain:AB line|genotype:ups39 CRISPR/Cas9 KO", "GSM8413282", "GSM8413282: Zebrafish  usp39  2; Danio rerio; RNA Seq", "GSM8413282 r1", "GSM8413282", "1", "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer's instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP521541", null, null, "usp39_2_S6_R1_001.fastq.gz", "fastq", 5258831648.0, 46953854.0, "GSM8413282 r1", "0:112", "A:1574548331;C:1105202446;G:1259800817;T:1318114513;N:1165541", 112, null, null, null, 1574548331, 1105202446, 1259800817, 1318114513, 1165541, "SRX25419303", "SRS22079474", "SRA1930695", "Institute of Biochemistry II", "Institute of Biochemistry II", 1, 0.57786, null, 0.22723, null, 0.71502, null, 0.46758, null, 112, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "rrna_depletion", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2024-07-23", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [33299, "SRR29925296", "SRX25419302", "SRS22079472", "SRP521541", "PRJNA1139080", "Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER Phagy", "GSE272836", "Transcriptome Analysis", "RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However  the regulatory mechanisms connecting these processes remain poorly understood. Here  we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic five prime splice sites. Importantly  disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. These spurious isoforms disrupt proteostasis causing cytosolic protein aggregates and ER stress. Proteotoxic exons activate unfolded protein response  causing CHOP mediated cell death. In response to impaired splicing  eukaryotic cells enhance ubiquitination and ER phagy to alleviate the pathogenic accumulation of proteotoxic isoforms. Our findings show how cryptic splicing induced proteotoxicity can be mitigated  and provide insight into the molecular pathogenesis of spliceosome associated diseases such as retinitis pigmentosa. Overall design: Comparative gene expression profiling analysis of RNA seq data for WT Zebrafish and its morpholino usp39 KD derivarive", null, "pubmed:39541449", null, "Zebrafish  usp39  1", "GSM8413281", null, "source name:whole organism|tissue:whole organism|strain:AB line|genotype:ups39 CRISPR/Cas9 KO|geo loc name:missing|collection date:missing", "Zebrafish  usp39  1", "BCL convert  v4.0.3 Sequence reads were trimmed for adaptor sequences/low quality sequences using Trimmomatic  v0.40 rc1  parameters ILLUMINACLIP: TruSeq3 SE.fa:2:30:10; CROP:111; HEADCROP:12 GENCODE annotation was used to map reads to the zebrafish genome version Danio rerio.GRCz11.110 with STAR  v2.7.11a  parameters:   runMode alignReads:   outSAMtype BAM SortedByCoordinate; Count reads into exons was determined by using the htseq count  v1.99.2 Differential gene expression analysis was done with DESeq2  v1.42.1 Assembly: Danio rerio.GRCz11.110 Supplementary files format and content: tab delminted text file includes raw count for each Sample", "whole organism", null, "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer\u2019s instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer\u2019s instructions.", null, "tissue:whole organism|strain:AB line|genotype:ups39 CRISPR/Cas9 KO", "GSM8413281", "GSM8413281: Zebrafish  usp39  1; Danio rerio; RNA Seq", "GSM8413281 r1", "GSM8413281", "1", "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer's instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP521541", null, null, "usp39_1_S5_R1_001.fastq.gz", "fastq", 6219261664.0, 55529122.0, "GSM8413281 r1", "0:112", "A:1884475909;C:1283923393;G:1434823696;T:1614670192;N:1368474", 112, null, null, null, 1884475909, 1283923393, 1434823696, 1614670192, 1368474, "SRX25419302", "SRS22079472", "SRA1930695", "Institute of Biochemistry II", "Institute of Biochemistry II", 1, 0.55692, null, 0.23871, null, 0.72368, null, 0.47061, null, 112, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "rrna_depletion", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2024-07-23", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [33300, "SRR29925298", "SRX25419301", "SRS22079473", "SRP521541", "PRJNA1139080", "Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER Phagy", "GSE272836", "Transcriptome Analysis", "RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However  the regulatory mechanisms connecting these processes remain poorly understood. Here  we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic five prime splice sites. Importantly  disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. These spurious isoforms disrupt proteostasis causing cytosolic protein aggregates and ER stress. Proteotoxic exons activate unfolded protein response  causing CHOP mediated cell death. In response to impaired splicing  eukaryotic cells enhance ubiquitination and ER phagy to alleviate the pathogenic accumulation of proteotoxic isoforms. Our findings show how cryptic splicing induced proteotoxicity can be mitigated  and provide insight into the molecular pathogenesis of spliceosome associated diseases such as retinitis pigmentosa. Overall design: Comparative gene expression profiling analysis of RNA seq data for WT Zebrafish and its morpholino usp39 KD derivarive", null, "pubmed:39541449", null, "Zebrafish  gfp  4", "GSM8413280", null, "source name:whole organism|tissue:whole organism|strain:AB line|genotype:WT|geo loc name:missing|collection date:missing", "Zebrafish  gfp  4", "BCL convert  v4.0.3 Sequence reads were trimmed for adaptor sequences/low quality sequences using Trimmomatic  v0.40 rc1  parameters ILLUMINACLIP: TruSeq3 SE.fa:2:30:10; CROP:111; HEADCROP:12 GENCODE annotation was used to map reads to the zebrafish genome version Danio rerio.GRCz11.110 with STAR  v2.7.11a  parameters:   runMode alignReads:   outSAMtype BAM SortedByCoordinate; Count reads into exons was determined by using the htseq count  v1.99.2 Differential gene expression analysis was done with DESeq2  v1.42.1 Assembly: Danio rerio.GRCz11.110 Supplementary files format and content: tab delminted text file includes raw count for each Sample", "whole organism", null, "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer\u2019s instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer\u2019s instructions.", null, "tissue:whole organism|strain:AB line|genotype:WT", "GSM8413280", "GSM8413280: Zebrafish  gfp  4; Danio rerio; RNA Seq", "GSM8413280 r1", "GSM8413280", "1", "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer's instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP521541", null, null, "gfp_4_S4_R1_001.fastq.gz", "fastq", 5026290192.0, 44877591.0, "GSM8413280 r1", "0:112", "A:1507589049;C:1029477633;G:1172973804;T:1315148479;N:1101227", 112, null, null, null, 1507589049, 1029477633, 1172973804, 1315148479, 1101227, "SRX25419301", "SRS22079473", "SRA1930695", "Institute of Biochemistry II", "Institute of Biochemistry II", 1, 0.62232, null, 0.2749, null, 0.70907, null, 0.45946, null, 112, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "rrna_depletion", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2024-07-23", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [33301, "SRR29925299", "SRX25419300", "SRS22079475", "SRP521541", "PRJNA1139080", "Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER Phagy", "GSE272836", "Transcriptome Analysis", "RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However  the regulatory mechanisms connecting these processes remain poorly understood. Here  we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic five prime splice sites. Importantly  disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. These spurious isoforms disrupt proteostasis causing cytosolic protein aggregates and ER stress. Proteotoxic exons activate unfolded protein response  causing CHOP mediated cell death. In response to impaired splicing  eukaryotic cells enhance ubiquitination and ER phagy to alleviate the pathogenic accumulation of proteotoxic isoforms. Our findings show how cryptic splicing induced proteotoxicity can be mitigated  and provide insight into the molecular pathogenesis of spliceosome associated diseases such as retinitis pigmentosa. Overall design: Comparative gene expression profiling analysis of RNA seq data for WT Zebrafish and its morpholino usp39 KD derivarive", null, "pubmed:39541449", null, "Zebrafish  gfp  3", "GSM8413279", null, "source name:whole organism|tissue:whole organism|strain:AB line|genotype:WT|geo loc name:missing|collection date:missing", "Zebrafish  gfp  3", "BCL convert  v4.0.3 Sequence reads were trimmed for adaptor sequences/low quality sequences using Trimmomatic  v0.40 rc1  parameters ILLUMINACLIP: TruSeq3 SE.fa:2:30:10; CROP:111; HEADCROP:12 GENCODE annotation was used to map reads to the zebrafish genome version Danio rerio.GRCz11.110 with STAR  v2.7.11a  parameters:   runMode alignReads:   outSAMtype BAM SortedByCoordinate; Count reads into exons was determined by using the htseq count  v1.99.2 Differential gene expression analysis was done with DESeq2  v1.42.1 Assembly: Danio rerio.GRCz11.110 Supplementary files format and content: tab delminted text file includes raw count for each Sample", "whole organism", null, "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer\u2019s instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer\u2019s instructions.", null, "tissue:whole organism|strain:AB line|genotype:WT", "GSM8413279", "GSM8413279: Zebrafish  gfp  3; Danio rerio; RNA Seq", "GSM8413279 r1", "GSM8413279", "1", "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer's instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP521541", null, null, "gfp_3_S3_R1_001.fastq.gz", "fastq", 6191810800.0, 55284025.0, "GSM8413279 r1", "0:112", "A:1881286910;C:1233644529;G:1388707003;T:1686807249;N:1365109", 112, null, null, null, 1881286910, 1233644529, 1388707003, 1686807249, 1365109, "SRX25419300", "SRS22079475", "SRA1930695", "Institute of Biochemistry II", "Institute of Biochemistry II", 1, 0.64098, null, 0.2934, null, 0.71151, null, 0.46325, null, 112, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "rrna_depletion", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2024-07-23", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [33302, "SRR29925300", "SRX25419299", "SRS22079476", "SRP521541", "PRJNA1139080", "Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER Phagy", "GSE272836", "Transcriptome Analysis", "RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However  the regulatory mechanisms connecting these processes remain poorly understood. Here  we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic five prime splice sites. Importantly  disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. These spurious isoforms disrupt proteostasis causing cytosolic protein aggregates and ER stress. Proteotoxic exons activate unfolded protein response  causing CHOP mediated cell death. In response to impaired splicing  eukaryotic cells enhance ubiquitination and ER phagy to alleviate the pathogenic accumulation of proteotoxic isoforms. Our findings show how cryptic splicing induced proteotoxicity can be mitigated  and provide insight into the molecular pathogenesis of spliceosome associated diseases such as retinitis pigmentosa. Overall design: Comparative gene expression profiling analysis of RNA seq data for WT Zebrafish and its morpholino usp39 KD derivarive", null, "pubmed:39541449", null, "Zebrafish  gfp  2", "GSM8413278", null, "source name:whole organism|tissue:whole organism|strain:AB line|genotype:WT|geo loc name:missing|collection date:missing", "Zebrafish  gfp  2", "BCL convert  v4.0.3 Sequence reads were trimmed for adaptor sequences/low quality sequences using Trimmomatic  v0.40 rc1  parameters ILLUMINACLIP: TruSeq3 SE.fa:2:30:10; CROP:111; HEADCROP:12 GENCODE annotation was used to map reads to the zebrafish genome version Danio rerio.GRCz11.110 with STAR  v2.7.11a  parameters:   runMode alignReads:   outSAMtype BAM SortedByCoordinate; Count reads into exons was determined by using the htseq count  v1.99.2 Differential gene expression analysis was done with DESeq2  v1.42.1 Assembly: Danio rerio.GRCz11.110 Supplementary files format and content: tab delminted text file includes raw count for each Sample", "whole organism", null, "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer\u2019s instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer\u2019s instructions.", null, "tissue:whole organism|strain:AB line|genotype:WT", "GSM8413278", "GSM8413278: Zebrafish  gfp  2; Danio rerio; RNA Seq", "GSM8413278 r1", "GSM8413278", "1", "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer's instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP521541", null, null, "gfp_2_S2_R1_001.fastq.gz", "fastq", 6342165088.0, 56626474.0, "GSM8413278 r1", "0:112", "A:1934945429;C:1301674304;G:1435430621;T:1668715260;N:1399474", 112, null, null, null, 1934945429, 1301674304, 1435430621, 1668715260, 1399474, "SRX25419299", "SRS22079476", "SRA1930695", "Institute of Biochemistry II", "Institute of Biochemistry II", 1, 0.61901, null, 0.26573, null, 0.70666, null, 0.47037, null, 112, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "rrna_depletion", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2024-07-23", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [33303, "SRR29925301", "SRX25419298", "SRS22079471", "SRP521541", "PRJNA1139080", "Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER Phagy", "GSE272836", "Transcriptome Analysis", "RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However  the regulatory mechanisms connecting these processes remain poorly understood. Here  we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic five prime splice sites. Importantly  disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. These spurious isoforms disrupt proteostasis causing cytosolic protein aggregates and ER stress. Proteotoxic exons activate unfolded protein response  causing CHOP mediated cell death. In response to impaired splicing  eukaryotic cells enhance ubiquitination and ER phagy to alleviate the pathogenic accumulation of proteotoxic isoforms. Our findings show how cryptic splicing induced proteotoxicity can be mitigated  and provide insight into the molecular pathogenesis of spliceosome associated diseases such as retinitis pigmentosa. Overall design: Comparative gene expression profiling analysis of RNA seq data for WT Zebrafish and its morpholino usp39 KD derivarive", null, "pubmed:39541449", null, "Zebrafish  gfp  1", "GSM8413277", null, "source name:whole organism|tissue:whole organism|strain:AB line|genotype:WT|geo loc name:missing|collection date:missing", "Zebrafish  gfp  1", "BCL convert  v4.0.3 Sequence reads were trimmed for adaptor sequences/low quality sequences using Trimmomatic  v0.40 rc1  parameters ILLUMINACLIP: TruSeq3 SE.fa:2:30:10; CROP:111; HEADCROP:12 GENCODE annotation was used to map reads to the zebrafish genome version Danio rerio.GRCz11.110 with STAR  v2.7.11a  parameters:   runMode alignReads:   outSAMtype BAM SortedByCoordinate; Count reads into exons was determined by using the htseq count  v1.99.2 Differential gene expression analysis was done with DESeq2  v1.42.1 Assembly: Danio rerio.GRCz11.110 Supplementary files format and content: tab delminted text file includes raw count for each Sample", "whole organism", null, "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer\u2019s instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer\u2019s instructions.", null, "tissue:whole organism|strain:AB line|genotype:WT", "GSM8413277", "GSM8413277: Zebrafish  gfp  1; Danio rerio; RNA Seq", "GSM8413277 r1", "GSM8413277", "1", "Samples were homogenized in 200 \u00b5l RNAzol\u00ae RT Sigma Aldrich in gentleMACS\u2122 M Tubes using gentleMACS\u2122 Octo Dissociator with Heaters Miltenyi Biotec  program RNA 02.01. RNA was extracted following the RNAzol\u00ae RT extraction protocol. Ribosomal RNA was depleted from 1.0 \u00b5g total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat Lexogen following the manufacturer's instructions. Sequencing libraries were generated using the CORALL RNA Seq kits Lexogen following the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP521541", null, null, "gfp_1_S1_R1_001.fastq.gz", "fastq", 5995698912.0, 53533026.0, "GSM8413277 r1", "0:112", "A:1785573790;C:1251424786;G:1355613253;T:1601762911;N:1324172", 112, null, null, null, 1785573790, 1251424786, 1355613253, 1601762911, 1324172, "SRX25419298", "SRS22079471", "SRA1930695", "Institute of Biochemistry II", "Institute of Biochemistry II", 1, 0.64323, null, 0.28918, null, 0.70857, null, 0.46537, null, 112, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "rrna_depletion", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2024-07-23", "Undetermined", "Undetermined", "Whole Organism", "All anatomical structures"], [36271, "SRR298568", "SRX079846", "SRS212652", "SRP007331", "PRJNA141525", "Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.", "GSE29418", "Transcriptome Analysis", "RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.", null, "pubmed:21743441", null, "ZiwiIPTes", "GSM727525", null, "tissue:RNA obtained from immunoprecipitation with Ziwi antibody from zebrafish testis extract|strain:TL", "ZiwiIPTes", "three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.", "RNA obtained from immunoprecipitation with Ziwi antibody from zebrafish testis extract", null, "Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 \u00c2\u00b5l Dynabeads Invitrogen  3 or 6 testes  and Ziwi antibody in a total volume of 500 \u00c2\u00b5l.  RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis  adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.", null, "strain:TL", "GSM727525", "GSM727525: ZiwiIPTes", "GSM727525: ZiwiIPTes", "GSM727525: ZiwiIPTes", "1", null, "GEO Accession:GSM727525", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP007331", null, "read name barcode proc directive:ignore", "ZiwiIPTes.fastq", "fastq", 976120596.0, 27114461.0, "GSM727525 1", "0:36", null, 36, null, null, null, null, null, null, null, null, "SRX079846", "SRS212652", "SRA039167", "GEO", "European Research Institute for the Biology of Ageing, University Medical Center Groningen", 1, 0.10415, null, 0.03658, null, 0.96173, null, 0.30033, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2011-05-20", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [36272, "SRR298567", "SRX079845", "SRS212651", "SRP007331", "PRJNA141525", "Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.", "GSE29418", "Transcriptome Analysis", "RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.", null, "pubmed:21743441", null, "ZiliIPTes", "GSM727524", null, "tissue:RNA obtained from immunoprecipitation with Zili antibody|strain:TL", "ZiliIPTes", "three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.", "RNA obtained from immunoprecipitation with Zili antibody", null, "Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 \u00c2\u00b5l Dynabeads Invitrogen  3 or 6 testes  and Zili antibody in a total volume of 500 \u00c2\u00b5l.  RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis  adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.", null, "strain:TL", "GSM727524", "GSM727524: ZiliIPTes", "GSM727524: ZiliIPTes", "GSM727524: ZiliIPTes", "1", null, "GEO Accession:GSM727524", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP007331", null, "read name barcode proc directive:ignore", "ZiliIPTes.fastq", "fastq", 995759064.0, 27659974.0, "GSM727524 1", "0:36", null, 36, null, null, null, null, null, null, null, null, "SRX079845", "SRS212651", "SRA039167", "GEO", "European Research Institute for the Biology of Ageing, University Medical Center Groningen", 1, 0.0537, null, 0.03117, null, 0.95856, null, 0.42091, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2011-05-20", "Undetermined", "Undetermined", "Trunk", "Surface Structure"], [36276, "SRR298563", "SRX079841", "SRS212647", "SRP007331", "PRJNA141525", "Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.", "GSE29418", "Transcriptome Analysis", "RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.", null, "pubmed:21743441", null, "TDRD1IPshort", "GSM727520", null, "tissue:RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract|strain:TL", "TDRD1IPshort", "three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.", "RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract", null, "Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 \u00c2\u00b5l Dynabeads Invitrogen  3 or 6 testes  and Tdrd1 antibody 1:100 in a total volume of 500 \u00c2\u00b5l.  RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis  adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.", null, "strain:TL", "GSM727520", "GSM727520: TDRD1IPshort", "GSM727520: TDRD1IPshort", "GSM727520: TDRD1IPshort", "1", null, "GEO Accession:GSM727520", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP007331", null, "read name barcode proc directive:ignore", "TDRD1IPshort.fastq", "fastq", 957724884.0, 26603469.0, "GSM727520 1", "0:36", null, 36, null, null, null, null, null, null, null, null, "SRX079841", "SRS212647", "SRA039167", "GEO", "European Research Institute for the Biology of Ageing, University Medical Center Groningen", 1, 0.10539, null, 0.05124, null, 0.93935, null, 0.34909, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2011-05-20", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [36277, "SRR298562", "SRX079840", "SRS212646", "SRP007331", "PRJNA141525", "Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.", "GSE29418", "Transcriptome Analysis", "RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.", null, "pubmed:21743441", null, "TDRD1IPlong", "GSM727519", null, "tissue:RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract|strain:TL", "TDRD1IPlong", "three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.", "RNA obtained from immunoprecipitation with Tdrd1 antibody from zebrafish testis extract", null, "Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 \u00c2\u00b5l Dynabeads Invitrogen  3 or 6 testes  and Tdrd1 antibody 1:100 in a total volume of 500 \u00c2\u00b5l.  For cDNA synthesis  the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.", null, "strain:TL", "GSM727519", "GSM727519: TDRD1IPlong", "GSM727519: TDRD1IPlong", "GSM727519: TDRD1IPlong", "1", null, "GEO Accession:GSM727519", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>46</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP007331", null, "read name barcode proc directive:ignore", "TDRD1IPlong.fastq", "fastq", 1098157770.0, 23872995.0, "GSM727519 1", "0:46", null, 46, null, null, null, null, null, null, null, null, "SRX079840", "SRS212646", "SRA039167", "GEO", "European Research Institute for the Biology of Ageing, University Medical Center Groningen", 1, 0.63282, null, 0.29001, null, 0.80095, null, 0.51046, null, 46, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2011-05-20", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [36285, "SRR363985", "SRX105298", "SRS270141", "SRP009275", "PRJNA148581", "Hen1 analysis in zebrafish", "GSE33582", "Transcriptome Analysis", "small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel  the small RNA libraries wre made.", null, "pubmed:20859253", null, "wildtype ligation", "GSM830247", null, "source name:testis|strain:TL|genotype/variation:Hen1 wildtype|tissue:testis|small rna library prep method:adapter ligation", "wildtype ligation", "three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8", "testis", null, "Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. Adaptors were ligated to the five prime and three prime ends of the isolated RNA  and the product was converted to cDNA using a primer on the three prime adaptor. post 15 cycles PCR amplification of the library the product was gel purified and sequenced on a Solexa platform.", null, "strain:TL|genotype/variation:Hen1 wildtype|tissue:testis|small rna library prep method:adapter ligation", "GSM830247", "GSM830247: wildtype ligation", "GSM830247: wildtype ligation", "GSM830247: wildtype ligation", "1", null, "GEO Accession:GSM830247", "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>46</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP009275", null, "read name barcode proc directive:ignore", "WTTESTIS.fastq", "fastq", 395791130.0, 8604155.0, "GSM830247 1", "0:46", "A:79045664;C:90489917;G:99082007;T:127024229;N:149313", 46, null, null, null, 79045664, 90489917, 99082007, 127024229, 149313, "SRX105298", "SRS270141", "SRA047996", "GEO", "European Research Institute for the Biology of Ageing, University Medical Center Groningen", 1, 0.00021, null, 0.00015, null, 0.99989, null, 0.0, null, 46, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "5prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2011-11-09", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [36286, "SRR363984", "SRX105297", "SRS270140", "SRP009275", "PRJNA148581", "Hen1 analysis in zebrafish", "GSE33582", "Transcriptome Analysis", "small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel  the small RNA libraries wre made.", null, "pubmed:20859253", null, "hen1 mutant ligation", "GSM830246", null, "source name:testis|strain:TL|genotype/variation:Hen1 mutant|tissue:testis|small rna library prep method:adapter ligation", "hen1 mutant ligation", "three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8", "testis", null, "Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. Adaptors were ligated to the five prime and three prime ends of the isolated RNA  and the product was converted to cDNA using a primer on the three prime adaptor. post 15 cycles PCR amplification of the library the product was gel purified and sequenced on a Solexa platform.", null, "strain:TL|genotype/variation:Hen1 mutant|tissue:testis|small rna library prep method:adapter ligation", "GSM830246", "GSM830246: hen1 mutant ligation", "GSM830246: hen1 mutant ligation", "GSM830246: hen1 mutant ligation", "1", null, "GEO Accession:GSM830246", "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>46</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP009275", null, "read name barcode proc directive:ignore", "HEN1TESTIS.fastq", "fastq", 440876374.0, 9584269.0, "GSM830246 1", "0:46", "A:91693980;C:99515953;G:105634029;T:143841954;N:190458", 46, null, null, null, 91693980, 99515953, 105634029, 143841954, 190458, "SRX105297", "SRS270140", "SRA047996", "GEO", "European Research Institute for the Biology of Ageing, University Medical Center Groningen", 1, 0.00039, null, 0.00033, null, 0.99995, null, 0.0, null, 46, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "5prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2011-11-09", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [36287, "SRR363983", "SRX105296", "SRS270139", "SRP009275", "PRJNA148581", "Hen1 analysis in zebrafish", "GSE33582", "Transcriptome Analysis", "small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel  the small RNA libraries wre made.", null, "pubmed:20859253", null, "wildtype polyA", "GSM830245", null, "source name:testis|strain:TL|genotype/variation:Hen1 wildtype|tissue:testis|small rna library prep method:polyA tailing", "wildtype polyA", "three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8", "testis", null, "Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. RNA was polyA tailed using polyA polymerase followed by ligation of a RNA adaptor to the five prime phosphate of the small RNAs. First strand cDNA synthesis was performed using an oligodT linker primer and M MLV RNase H  reverse transcriptase. post amplification the cDNA was sent for sequencing on an Illumina/Solexa platform.", null, "strain:TL|genotype/variation:Hen1 wildtype|tissue:testis|small rna library prep method:polyA tailing", "GSM830245", "GSM830245: wildtype polyA", "GSM830245: wildtype polyA", "GSM830245: wildtype polyA", "1", null, "GEO Accession:GSM830245", "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>44</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP009275", null, "read name barcode proc directive:ignore", "VASAGFPHEN1plusMALE.fastq", "fastq", 167344144.0, 3803276.0, "GSM830245 1", "0:44", "A:87935982;C:21182538;G:19081938;T:34474815;N:4668871", 44, null, null, null, 87935982, 21182538, 19081938, 34474815, 4668871, "SRX105296", "SRS270139", "SRA047996", "GEO", "European Research Institute for the Biology of Ageing, University Medical Center Groningen", 1, 0.06642, null, 0.05042, null, 0.99226, null, 0.38346, null, 44, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2011-11-09", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [36288, "SRR363982", "SRX105295", "SRS270138", "SRP009275", "PRJNA148581", "Hen1 analysis in zebrafish", "GSE33582", "Transcriptome Analysis", "small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel  the small RNA libraries wre made.", null, "pubmed:20859253", null, "hen1 mutant polyA", "GSM830244", null, "source name:testis|strain:TL|genotype/variation:Hen1 mutant|tissue:testis|small rna library prep method:polyA tailing", "hen1 mutant polyA", "three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8", "testis", null, "Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. RNA was polyA tailed using polyA polymerase followed by ligation of a RNA adaptor to the five prime phosphate of the small RNAs. First strand cDNA synthesis was performed using an oligodT linker primer and M MLV RNase H  reverse transcriptase. post amplification the cDNA was sent for sequencing on an Illumina/Solexa platform.", null, "strain:TL|genotype/variation:Hen1 mutant|tissue:testis|small rna library prep method:polyA tailing", "GSM830244", "GSM830244: hen1 mutant polyA", "GSM830244: hen1 mutant polyA", "GSM830244: hen1 mutant polyA", "1", null, "GEO Accession:GSM830244", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>44</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP009275", null, "read name barcode proc directive:ignore", "VASAGFPHEN1minusMALE.fastq", "fastq", 267208964.0, 6072931.0, "GSM830244 1", "0:44", "A:143478691;C:30051676;G:33682677;T:59883224;N:112696", 44, null, null, null, 143478691, 30051676, 33682677, 59883224, 112696, "SRX105295", "SRS270138", "SRA047996", "GEO", "European Research Institute for the Biology of Ageing, University Medical Center Groningen", 1, 0.01616, null, 0.01033, null, 0.99381, null, 0.76337, null, 44, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2011-11-09", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [36504, "SRR535848", "SRX174964", "SRS352998", "SRP014772", "PRJNA172016", "Danio rerio strain:*AB Variation", "PRJNA172016", "Other", "Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life  however identifying the causal mutations from such screens has long been the bottleneck in the process  particularly in vertebrates. We have developed an RNA Seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons  alter transcript splicing  or alter gene expression levels. Furthermore  we develop an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall  we show that RNA Seq is a fast  reliable  and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.", null, null, "RNA seq data from Miller et al submitted. Data was generated in order to map ENU induced mutations in zebrafish. This data hox20 was created from 20 pooled hoxb1bb1219 fish that were the siblings of wt20.", "Miller hox20.bam", "Miller hox20.bam", null, null, null, null, null, null, null, null, null, null, "Miller hox20.bam", "Miller hox20.bam", "1", "50 bp Paired End", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>180</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP014772", null, null, "hox20.bam", "bam", 2051648571.0, 22151528.0, "Miller hox20.bam", "0:49 1:49", "A:528770281;C:501621137;G:487051170;T:534176088;N:29895", 49, 49, null, null, 528770281, 501621137, 487051170, 534176088, 29895, "SRX174964", "SRS352998", "SRA056859", "Fred Hutchinson Cancer Research Center|Moens", "Fred Hutchinson Cancer Research Center", 2, 0.9629, 0.96282, 0.07314, 0.07288, 0.6714, 0.67125, 0.4665, 0.4637, 49, 49, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2012-11-30", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [36739, "SRR867022", "SRX286270", "SRS420566", "SRP022549", "PRJNA202401", "Danio rerio Transcriptome or Gene expression", "PRJNA202401", "Other", "Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.", null, null, "Full transcriptome analysis of early dorsoventral DV patterning in zebrafish", "General Sample for Danio rerio", "ICH", null, "strain:wild type", null, null, null, null, null, null, null, null, "Full transcriptome analysis of early dorsoventral DV patterning in zebrafish  Bcat", "Danio rerio boot", "1", "RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies  according to the manufacturers suggestions. Briefly  5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII  the 50 200nt fraction size selected  sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol  and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP022549", null, null, "s0205_20091123_4_Boot2_F3_QV.qual s0205_20091123_4_Boot2_F3.csfasta", "SOLiD_native SOLiD_native", 9801985250.0, 196039705.0, "Zebrafish DV patterning Boot", "0:50", "0:2587797600;1:2275478534;2:2625317272;3:2293877905;.:19513939", 50, null, null, null, null, null, null, null, null, "SRX286270", "SRS420566", "SRA075737", "BAYGEN|NGSP", "BAYGEN", 1, 0.59289, null, 0.09435, null, 0.92669, null, 0.7658, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "3prime", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2013-05-23", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [36740, "SRR867023", "SRX286271", "SRS420566", "SRP022549", "PRJNA202401", "Danio rerio Transcriptome or Gene expression", "PRJNA202401", "Other", "Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.", null, null, "Full transcriptome analysis of early dorsoventral DV patterning in zebrafish", "General Sample for Danio rerio", "ICH", null, "strain:wild type", null, null, null, null, null, null, null, null, "Full transcriptome analysis of early dorsoventral DV patterning in zebrafish  ICH", "Danio rerio ICH", "1", "RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies  according to the manufacturers suggestions. Briefly  5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII  the 50 200nt fraction size selected  sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol  and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP022549", null, null, "s0205_20091123_4_ICH_F3.csfasta s0205_20091123_4_ICH_F3_QV.qual", "SOLiD_native SOLiD_native", 10810535400.0, 216210708.0, "Zebrafish DV patterning ICH", "0:50", "0:2903579857;1:2528898611;2:2759865128;3:2553918387;.:64273417", 50, null, null, null, null, null, null, null, null, "SRX286271", "SRS420566", "SRA075737", "BAYGEN|NGSP", "BAYGEN", 1, 0.42474, null, 0.06136, null, 0.93434, null, 0.75757, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "3prime", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2013-05-23", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [37134, "SRR997335", "SRX355601", "SRS483796", "SRP030036", "PRJNA219641", "Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways", "GSE51018", "Transcriptome Analysis", "The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition", "parent bioproject:PRJNA219631", "pubmed:26857418", null, "Heart  Control  rep4", "GSM1234963", null, "source name:Heart  Control|tissue:heart", "Heart  Control  rep4", "Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format", "Heart  Control", null, "Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001", null, "tissue:heart", "GSM1234963", "GSM1234963: Heart  Control  rep4; Danio rerio; RNA Seq", "GSM1234963", null, "1", "Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001", "GEO Accession:GSM1234963", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP030036", null, null, "C3PO_0053_s_7_sequence.txt.gz", "fastq", 1111882122.0, 28509798.0, "GSM1234963 r1", "0:39", "A:239964076;C:229590501;G:337557042;T:303257677;N:1512826", 39, null, null, null, 239964076, 229590501, 337557042, 303257677, 1512826, "SRX355601", "SRS483796", "SRA101779", "GEO", "Vital-IT, SIB Swiss Institute of Bioinformatics", 1, 0.11195, null, 0.03776, null, 0.98871, null, 0.16576, null, 39, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "Switzerland", "2013-09-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [37135, "SRR997334", "SRX355600", "SRS483795", "SRP030036", "PRJNA219641", "Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways", "GSE51018", "Transcriptome Analysis", "The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition", "parent bioproject:PRJNA219631", "pubmed:26857418", null, "Heart  Control  rep3", "GSM1234962", null, "source name:Heart  Control|tissue:heart", "Heart  Control  rep3", "Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format", "Heart  Control", null, "Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001", null, "tissue:heart", "GSM1234962", "GSM1234962: Heart  Control  rep3; Danio rerio; RNA Seq", "GSM1234962", null, "1", "Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001", "GEO Accession:GSM1234962", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP030036", null, null, "C3PO_0053_s_6_sequence.txt.gz", "fastq", 1221305046.0, 31315514.0, "GSM1234962 r1", "0:39", "A:263520584;C:251263128;G:372262308;T:332218529;N:2040497", 39, null, null, null, 263520584, 251263128, 372262308, 332218529, 2040497, "SRX355600", "SRS483795", "SRA101779", "GEO", "Vital-IT, SIB Swiss Institute of Bioinformatics", 1, 0.11552, null, 0.03865, null, 0.98679, null, 0.1927, null, 39, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "Switzerland", "2013-09-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [37136, "SRR997333", "SRX355599", "SRS483794", "SRP030036", "PRJNA219641", "Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways", "GSE51018", "Transcriptome Analysis", "The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition", "parent bioproject:PRJNA219631", "pubmed:26857418", null, "Heart  Control  rep2", "GSM1234961", null, "source name:Heart  Control|tissue:heart", "Heart  Control  rep2", "Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format", "Heart  Control", null, "Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001", null, "tissue:heart", "GSM1234961", "GSM1234961: Heart  Control  rep2; Danio rerio; RNA Seq", "GSM1234961", null, "1", "Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001", "GEO Accession:GSM1234961", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP030036", null, null, "R2D2_0122_s_7_sequence.txt.gz", "fastq", 1462542939.0, 37501101.0, "GSM1234961 r1", "0:39", "A:313173840;C:298865755;G:440814004;T:409066990;N:622350", 39, null, null, null, 313173840, 298865755, 440814004, 409066990, 622350, "SRX355599", "SRS483794", "SRA101779", "GEO", "Vital-IT, SIB Swiss Institute of Bioinformatics", 1, 0.01745, null, 0.00554, null, 0.99101, null, 0.42928, null, 39, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "Switzerland", "2013-09-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [37137, "SRR997332", "SRX355598", "SRS483793", "SRP030036", "PRJNA219641", "Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways", "GSE51018", "Transcriptome Analysis", "The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition", "parent bioproject:PRJNA219631", "pubmed:26857418", null, "Heart  Control  rep1", "GSM1234960", null, "source name:Heart  Control|tissue:heart", "Heart  Control  rep1", "Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format", "Heart  Control", null, "Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001", null, "tissue:heart", "GSM1234960", "GSM1234960: Heart  Control  rep1; Danio rerio; RNA Seq", "GSM1234960", null, "1", "Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001", "GEO Accession:GSM1234960", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP030036", null, null, "R2D2_0122_s_6_sequence.txt.gz", "fastq", 1447346355.0, 37111445.0, "GSM1234960 r1", "0:39", "A:311132663;C:297266985;G:441400778;T:396960907;N:585022", 39, null, null, null, 311132663, 297266985, 441400778, 396960907, 585022, "SRX355598", "SRS483793", "SRA101779", "GEO", "Vital-IT, SIB Swiss Institute of Bioinformatics", 1, 0.06118, null, 0.01997, null, 0.98752, null, 0.43741, null, 39, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "Switzerland", "2013-09-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [37138, "SRR997331", "SRX355597", "SRS483792", "SRP030036", "PRJNA219641", "Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways", "GSE51018", "Transcriptome Analysis", "The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition", "parent bioproject:PRJNA219631", "pubmed:26857418", null, "Heart  Resected  rep4", "GSM1234959", null, "source name:Heart  Resected|tissue:heart", "Heart  Resected  rep4", "Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format", "Heart  Resected", null, "Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001", null, "tissue:heart", "GSM1234959", "GSM1234959: Heart  Resected  rep4; Danio rerio; RNA Seq", "GSM1234959", null, "1", "Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001", "GEO Accession:GSM1234959", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP030036", null, null, "C3PO_0053_s_5_sequence.txt.gz", "fastq", 703519557.0, 18038963.0, "GSM1234959 r1", "0:39", "A:142685665;C:144259439;G:215526965;T:199924689;N:1122799", 39, null, null, null, 142685665, 144259439, 215526965, 199924689, 1122799, "SRX355597", "SRS483792", "SRA101779", "GEO", "Vital-IT, SIB Swiss Institute of Bioinformatics", 1, 0.00172, null, 0.00045, null, 0.99738, null, 0.34873, null, 39, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "Switzerland", "2013-09-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [37139, "SRR997330", "SRX355596", "SRS483791", "SRP030036", "PRJNA219641", "Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways", "GSE51018", "Transcriptome Analysis", "The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition", "parent bioproject:PRJNA219631", "pubmed:26857418", null, "Heart  Resected  rep3", "GSM1234958", null, "source name:Heart  Resected|tissue:heart", "Heart  Resected  rep3", "Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format", "Heart  Resected", null, "Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001", null, "tissue:heart", "GSM1234958", "GSM1234958: Heart  Resected  rep3; Danio rerio; RNA Seq", "GSM1234958", null, "1", "Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001", "GEO Accession:GSM1234958", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP030036", null, null, "C3PO_0053_s_4_sequence.txt.gz", "fastq", 918978177.0, 23563543.0, "GSM1234958 r1", "0:39", "A:188056254;C:191217660;G:283318445;T:255042736;N:1343082", 39, null, null, null, 188056254, 191217660, 283318445, 255042736, 1343082, "SRX355596", "SRS483791", "SRA101779", "GEO", "Vital-IT, SIB Swiss Institute of Bioinformatics", 1, 0.09453, null, 0.03085, null, 0.98559, null, 0.18337, null, 39, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "Switzerland", "2013-09-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [37140, "SRR997329", "SRX355595", "SRS483789", "SRP030036", "PRJNA219641", "Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways", "GSE51018", "Transcriptome Analysis", "The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition", "parent bioproject:PRJNA219631", "pubmed:26857418", null, "Heart  Resected  rep2", "GSM1234957", null, "source name:Heart  Resected|tissue:heart", "Heart  Resected  rep2", "Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format", "Heart  Resected", null, "Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001", null, "tissue:heart", "GSM1234957", "GSM1234957: Heart  Resected  rep2; Danio rerio; RNA Seq", "GSM1234957", null, "1", "Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001", "GEO Accession:GSM1234957", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP030036", null, null, "R2D2_0122_s_5_sequence.txt.gz", "fastq", 1420874247.0, 36432673.0, "GSM1234957 r1", "0:39", "A:290914118;C:295973738;G:440368910;T:393019696;N:597785", 39, null, null, null, 290914118, 295973738, 440368910, 393019696, 597785, "SRX355595", "SRS483789", "SRA101779", "GEO", "Vital-IT, SIB Swiss Institute of Bioinformatics", 1, 0.00472, null, 0.00131, null, 0.99431, null, 0.42832, null, 39, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "Switzerland", "2013-09-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [37141, "SRR997328", "SRX355594", "SRS483790", "SRP030036", "PRJNA219641", "Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA dependent repair pathways", "GSE51018", "Transcriptome Analysis", "The mammalian heart has poor regenerative capacity following injury. In contrast  certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA dependant regulatory circuits in the heart. We identified novel miRNA dependant networks involved in critical biological pathways  which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart. Overall design: 2 conditions  4 biological replicates per condition", "parent bioproject:PRJNA219631", "pubmed:26857418", null, "Heart  Resected  rep1", "GSM1234956", null, "source name:Heart  Resected|tissue:heart", "Heart  Resected  rep1", "Base calling was with Illumina GAP Pipeline Software v1.70 Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX Toolkit Sequences were aligned to mouse mature microRNA sequences from miRBase Version 17 and non coding RNA sequences Rfam Version 10 using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as a/q x p where a= alignment length  q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches based on % query were selected. If a sequence had more than one top match against different database sequences  it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase. Genome build: miRBase17 Supplementary files format and content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq  estimateSizeFactors function. Count data are provided in tab delimited format", "Heart  Resected", null, "Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001", null, "tissue:heart", "GSM1234956", "GSM1234956: Heart  Resected  rep1; Danio rerio; RNA Seq", "GSM1234956", null, "1", "Total RNA was isolated using Trizol Invitrogen. RNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND 1000 spectrophotometer or an Agilent 2100 Bioanalyzer. Libraries of small RNAs for sequencing were prepared using the DGE Small RNA Sample Kit  Alternative v1.5 Protocol Illumina; San Diego  California according to the protocol supplied with the reagents Protocol Rev. A  published February 2009 and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx Illumina using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents Catalog FC 104 5020 and GD 300 1001", "GEO Accession:GSM1234956", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP030036", null, null, "C3PO_0054_s_8_sequence.txt.gz", "fastq", 1073339514.0, 27521526.0, "GSM1234956 r1", "0:39", "A:223670054;C:219603945;G:328718329;T:300891777;N:455409", 39, null, null, null, 223670054, 219603945, 328718329, 300891777, 455409, "SRX355594", "SRS483790", "SRA101779", "GEO", "Vital-IT, SIB Swiss Institute of Bioinformatics", 1, 0.05133, null, 0.01643, null, 0.9893, null, 0.25792, null, 39, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "Switzerland", "2013-09-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [39625, "SRR1920171", "SRX960487", "SRS877482", "SRP056356", "PRJNA278935", "Transcriptome profiling from the brain of male and female zebrafish", "GSE67092", "Transcriptome Analysis", "Genome wide analysis  to identify sex specific transcripts in the brain of male and female zebrafish Overall design: Examination of sex specific gene expression in the brain of male vs female zebrafish.", null, null, null, "RZB0003 Female", "GSM1638735", null, "source name:Female brain tissue|genotype:Wild type|Sex:female|tissue:Brain", "RZB0003 Female", "Illumina Casava1.8.2 software used for basecalling. Sequenced reads were uniquely mapped to Zv9 genome using tophat v1.4.1. Mapped reads were filtered of reads duplication  quality threshold <= 30  and loaded to Genespring  NGS Reads per kilobase per megabase RPKM was calculated  and normalized using  the DeSeq normalization procedure. Genome build: Zv9 Supplementary files format and content: tab delimited text files include Raw RPKM values and normalized RPKM for each Sample.", "Female brain tissue", null, "Brain from Male and female fish were extracted for RNA extraction. Brain tissues from 5 fish were collected and pooled. RNA Seq library preparation protocol: Total RNA was extracted using TRIzol\u00ae Reagent Invitrogen  USA. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. The integrity of RNA samples was determined using an Agilent RNA 6000 Nano chip on an Agilent 2100 Bioanalyzer. Samples with RNA Integrity Number RIN value of 8 9 was used for RNA seq library preparation. Messenger RNA sequencing library was prepared using TruSeq total RNA sample preparation kit Illumina; Total RNA sample preparation guide as per the manufacturers instructions with 3 microgram input RNA per library. Quality of RNA seq library was checked following company recommended protocols. RNA sequencing of male and female samples were performed on the Illumina HiSeq2000 Illumina  USA one sample per lane machine with single ended 51 bp read length.", null, "genotype:Wild type|Sex:female|tissue:Brain", "GSM1638735", "GSM1638735: RZB0003 Female; Danio rerio; RNA Seq", "GSM1638735", null, "1", "Brain from Male and female fish were extracted for RNA extraction. Brain tissues from 5 fish were collected and pooled. RNA Seq library preparation protocol: Total RNA was extracted using TRIzol\u00ae Reagent Invitrogen  USA. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. The integrity of RNA samples was determined using an Agilent RNA 6000 Nano chip on an Agilent 2100 Bioanalyzer. Samples with RNA Integrity Number RIN value of 8 9 was used for RNA seq library preparation. Messenger RNA sequencing library was prepared using TruSeq total RNA sample preparation kit Illumina; Total RNA sample preparation guide as per the manufacturers instructions with 3 microgram input RNA per library. Quality of RNA seq library was checked following company recommended protocols. RNA sequencing of male and female samples were performed on the Illumina HiSeq2000 Illumina  USA one sample per lane machine with single ended 51 bp read length.", "GEO Accession:GSM1638735", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP056356", null, null, "RZB003_NoIndex_L004_R1_All.fastq.gz", "fastq", 14531005592.0, 191197442.0, "GSM1638735 r1", "0:76", "A:4108884359;C:3166835425;G:3143573307;T:4098665685;N:13046816", 76, null, null, null, 4108884359, 3166835425, 3143573307, 4098665685, 13046816, "SRX960487", "SRS877482", "SRA247878", "GEO", "Computational and Systems Biology, Genome Institute of Singapore", 1, 0.91338, null, 0.17886, null, 0.69049, null, 0.5006, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2015-03-20", "Undetermined", "Undetermined", "Brain", "Nervous System"], [39626, "SRR1920170", "SRX960486", "SRS877483", "SRP056356", "PRJNA278935", "Transcriptome profiling from the brain of male and female zebrafish", "GSE67092", "Transcriptome Analysis", "Genome wide analysis  to identify sex specific transcripts in the brain of male and female zebrafish Overall design: Examination of sex specific gene expression in the brain of male vs female zebrafish.", null, null, null, "RZB0002 Male", "GSM1638734", null, "source name:Male brain tissue|genotype:Wild type|Sex:male|tissue:Brain", "RZB0002 Male", "Illumina Casava1.8.2 software used for basecalling. Sequenced reads were uniquely mapped to Zv9 genome using tophat v1.4.1. Mapped reads were filtered of reads duplication  quality threshold <= 30  and loaded to Genespring  NGS Reads per kilobase per megabase RPKM was calculated  and normalized using  the DeSeq normalization procedure. Genome build: Zv9 Supplementary files format and content: tab delimited text files include Raw RPKM values and normalized RPKM for each Sample.", "Male brain tissue", null, "Brain from Male and female fish were extracted for RNA extraction. Brain tissues from 5 fish were collected and pooled. RNA Seq library preparation protocol: Total RNA was extracted using TRIzol\u00ae Reagent Invitrogen  USA. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. The integrity of RNA samples was determined using an Agilent RNA 6000 Nano chip on an Agilent 2100 Bioanalyzer. Samples with RNA Integrity Number RIN value of 8 9 was used for RNA seq library preparation. Messenger RNA sequencing library was prepared using TruSeq total RNA sample preparation kit Illumina; Total RNA sample preparation guide as per the manufacturers instructions with 3 microgram input RNA per library. Quality of RNA seq library was checked following company recommended protocols. RNA sequencing of male and female samples were performed on the Illumina HiSeq2000 Illumina  USA one sample per lane machine with single ended 51 bp read length.", null, "genotype:Wild type|Sex:male|tissue:Brain", "GSM1638734", "GSM1638734: RZB0002 Male; Danio rerio; RNA Seq", "GSM1638734", null, "1", "Brain from Male and female fish were extracted for RNA extraction. Brain tissues from 5 fish were collected and pooled. RNA Seq library preparation protocol: Total RNA was extracted using TRIzol\u00ae Reagent Invitrogen  USA. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. The integrity of RNA samples was determined using an Agilent RNA 6000 Nano chip on an Agilent 2100 Bioanalyzer. Samples with RNA Integrity Number RIN value of 8 9 was used for RNA seq library preparation. Messenger RNA sequencing library was prepared using TruSeq total RNA sample preparation kit Illumina; Total RNA sample preparation guide as per the manufacturers instructions with 3 microgram input RNA per library. Quality of RNA seq library was checked following company recommended protocols. RNA sequencing of male and female samples were performed on the Illumina HiSeq2000 Illumina  USA one sample per lane machine with single ended 51 bp read length.", "GEO Accession:GSM1638734", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP056356", null, null, "RZB002_NoIndex_L001_R1_All.fastq.gz", "fastq", 14711238148.0, 193568923.0, "GSM1638734 r1", "0:76", "A:4154125162;C:3219757523;G:3187842434;T:4138123659;N:11389370", 76, null, null, null, 4154125162, 3219757523, 3187842434, 4138123659, 11389370, "SRX960486", "SRS877483", "SRA247878", "GEO", "Computational and Systems Biology, Genome Institute of Singapore", 1, 0.91063, null, 0.20427, null, 0.70183, null, 0.50769, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2015-03-20", "Undetermined", "Undetermined", "Brain", "Nervous System"], [39680, "SRR2039721", "SRX1038073", "SRS945231", "SRP058706", "PRJNA284916", "Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2", "GSE69219", "Other", "The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2  resulting in red shifted spectral sensitivity of the visual system.  We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone  so we profiled the RPE from TH  and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina  but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach  we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets  and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE  conducted in triplicate", null, "pubmed:26549260", null, "zebrafish RPE V3", "GSM1695527", null, "source name:retinal pigment epithelium RPE|treatment:Vehicle control|region of rpe:N/A|tissue:retinal pigment epithelium", "zebrafish RPE V3", "bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa  trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One  2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset  curated zebrafish transcriptome with cyp27 family transcripts added PLoS One  2013. 87: p. e67801  included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript  as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data", "retinal pigment epithelium RPE", null, "Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.", "Zebrafish were treated for three weeks with TH or a vehicle control.", "treatment:Vehicle control|region of rpe:N/A|tissue:retinal pigment epithelium", "GSM1695527", "GSM1695527: zebrafish RPE V3; Danio rerio; RNA Seq", "GSM1695527", null, "1", "Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.", "GEO Accession:GSM1695527", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP058706", null, null, "zebrafish_RPE_V3.fq.gz", "fastq", 1398879800.0, 27977596.0, "GSM1695527 r1", "0:50", "A:372827112;C:318907071;G:322799013;T:383834897;N:511707", 50, null, null, null, 372827112, 318907071, 322799013, 383834897, 511707, "SRX1038073", "SRS945231", "SRA269915", "GEO", "Washington University School of Medicine", 1, 0.86882, null, 0.25203, null, 0.75572, null, 0.65651, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-05-26", "Undetermined", "Undetermined", "Eye", "Sensory System"], [39681, "SRR2039720", "SRX1038072", "SRS945232", "SRP058706", "PRJNA284916", "Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2", "GSE69219", "Other", "The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2  resulting in red shifted spectral sensitivity of the visual system.  We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone  so we profiled the RPE from TH  and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina  but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach  we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets  and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE  conducted in triplicate", null, "pubmed:26549260", null, "zebrafish RPE V2", "GSM1695526", null, "source name:retinal pigment epithelium RPE|treatment:Vehicle control|region of rpe:N/A|tissue:retinal pigment epithelium", "zebrafish RPE V2", "bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa  trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One  2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset  curated zebrafish transcriptome with cyp27 family transcripts added PLoS One  2013. 87: p. e67801  included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript  as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data", "retinal pigment epithelium RPE", null, "Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.", "Zebrafish were treated for three weeks with TH or a vehicle control.", "treatment:Vehicle control|region of rpe:N/A|tissue:retinal pigment epithelium", "GSM1695526", "GSM1695526: zebrafish RPE V2; Danio rerio; RNA Seq", "GSM1695526", null, "1", "Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.", "GEO Accession:GSM1695526", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP058706", null, null, "zebrafish_RPE_V2.fq.gz", "fastq", 1424267450.0, 28485349.0, "GSM1695526 r1", "0:50", "A:384966484;C:318922158;G:323424610;T:396433148;N:521050", 50, null, null, null, 384966484, 318922158, 323424610, 396433148, 521050, "SRX1038072", "SRS945232", "SRA269915", "GEO", "Washington University School of Medicine", 1, 0.85592, null, 0.26231, null, 0.74614, null, 0.63068, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-05-26", "Undetermined", "Undetermined", "Eye", "Sensory System"], [39682, "SRR2039719", "SRX1038071", "SRS945233", "SRP058706", "PRJNA284916", "Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2", "GSE69219", "Other", "The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2  resulting in red shifted spectral sensitivity of the visual system.  We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone  so we profiled the RPE from TH  and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina  but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach  we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets  and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE  conducted in triplicate", null, "pubmed:26549260", null, "zebrafish RPE V1", "GSM1695525", null, "source name:retinal pigment epithelium RPE|treatment:Vehicle control|region of rpe:N/A|tissue:retinal pigment epithelium", "zebrafish RPE V1", "bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa  trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One  2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset  curated zebrafish transcriptome with cyp27 family transcripts added PLoS One  2013. 87: p. e67801  included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript  as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data", "retinal pigment epithelium RPE", null, "Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.", "Zebrafish were treated for three weeks with TH or a vehicle control.", "treatment:Vehicle control|region of rpe:N/A|tissue:retinal pigment epithelium", "GSM1695525", "GSM1695525: zebrafish RPE V1; Danio rerio; RNA Seq", "GSM1695525", null, "1", "Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.", "GEO Accession:GSM1695525", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP058706", null, null, "zebrafish_RPE_V1.fq.gz", "fastq", 1562666150.0, 31253323.0, "GSM1695525 r1", "0:50", "A:425809315;C:346680173;G:352748774;T:436855950;N:571938", 50, null, null, null, 425809315, 346680173, 352748774, 436855950, 571938, "SRX1038071", "SRS945233", "SRA269915", "GEO", "Washington University School of Medicine", 1, 0.8622, null, 0.24448, null, 0.74659, null, 0.63481, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-05-26", "Undetermined", "Undetermined", "Eye", "Sensory System"], [39683, "SRR2039718", "SRX1038070", "SRS945234", "SRP058706", "PRJNA284916", "Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2", "GSE69219", "Other", "The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2  resulting in red shifted spectral sensitivity of the visual system.  We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone  so we profiled the RPE from TH  and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina  but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach  we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets  and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE  conducted in triplicate", null, "pubmed:26549260", null, "zebrafish RPE T3", "GSM1695524", null, "source name:retinal pigment epithelium RPE|treatment:Thyroid horm1|region of rpe:N/A|tissue:retinal pigment epithelium", "zebrafish RPE T3", "bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa  trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One  2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset  curated zebrafish transcriptome with cyp27 family transcripts added PLoS One  2013. 87: p. e67801  included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript  as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data", "retinal pigment epithelium RPE", null, "Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.", "Zebrafish were treated for three weeks with TH or a vehicle control.", "treatment:Thyroid horm1|region of rpe:N/A|tissue:retinal pigment epithelium", "GSM1695524", "GSM1695524: zebrafish RPE T3; Danio rerio; RNA Seq", "GSM1695524", null, "1", "Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.", "GEO Accession:GSM1695524", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP058706", null, null, "zebrafish_RPE_T3.fq.gz", "fastq", 1384311250.0, 27686225.0, "GSM1695524 r1", "0:50", "A:365623713;C:318733172;G:322931194;T:376515371;N:507800", 50, null, null, null, 365623713, 318733172, 322931194, 376515371, 507800, "SRX1038070", "SRS945234", "SRA269915", "GEO", "Washington University School of Medicine", 1, 0.86222, null, 0.24783, null, 0.76124, null, 0.64632, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-05-26", "Undetermined", "Undetermined", "Eye", "Sensory System"], [39684, "SRR2039717", "SRX1038069", "SRS945235", "SRP058706", "PRJNA284916", "Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2", "GSE69219", "Other", "The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2  resulting in red shifted spectral sensitivity of the visual system.  We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone  so we profiled the RPE from TH  and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina  but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach  we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets  and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE  conducted in triplicate", null, "pubmed:26549260", null, "zebrafish RPE T2", "GSM1695523", null, "source name:retinal pigment epithelium RPE|treatment:Thyroid horm1|region of rpe:N/A|tissue:retinal pigment epithelium", "zebrafish RPE T2", "bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa  trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One  2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset  curated zebrafish transcriptome with cyp27 family transcripts added PLoS One  2013. 87: p. e67801  included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript  as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data", "retinal pigment epithelium RPE", null, "Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.", "Zebrafish were treated for three weeks with TH or a vehicle control.", "treatment:Thyroid horm1|region of rpe:N/A|tissue:retinal pigment epithelium", "GSM1695523", "GSM1695523: zebrafish RPE T2; Danio rerio; RNA Seq", "GSM1695523", null, "1", "Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.", "GEO Accession:GSM1695523", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP058706", null, null, "zebrafish_RPE_T2.fq.gz", "fastq", 1519161100.0, 30383222.0, "GSM1695523 r1", "0:50", "A:400594372;C:350805128;G:354718825;T:412492575;N:550200", 50, null, null, null, 400594372, 350805128, 354718825, 412492575, 550200, "SRX1038069", "SRS945235", "SRA269915", "GEO", "Washington University School of Medicine", 1, 0.86836, null, 0.26137, null, 0.75022, null, 0.60251, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-05-26", "Undetermined", "Undetermined", "Eye", "Sensory System"], [39685, "SRR2039716", "SRX1038068", "SRS945236", "SRP058706", "PRJNA284916", "Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2", "GSE69219", "Other", "The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2  resulting in red shifted spectral sensitivity of the visual system.  We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone  so we profiled the RPE from TH  and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina  but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach  we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets  and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE  conducted in triplicate", null, "pubmed:26549260", null, "zebrafish RPE T1", "GSM1695522", null, "source name:retinal pigment epithelium RPE|treatment:Thyroid horm1|region of rpe:N/A|tissue:retinal pigment epithelium", "zebrafish RPE T1", "bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa  trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One  2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset  curated zebrafish transcriptome with cyp27 family transcripts added PLoS One  2013. 87: p. e67801  included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript  as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data", "retinal pigment epithelium RPE", null, "Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.", "Zebrafish were treated for three weeks with TH or a vehicle control.", "treatment:Thyroid horm1|region of rpe:N/A|tissue:retinal pigment epithelium", "GSM1695522", "GSM1695522: zebrafish RPE T1; Danio rerio; RNA Seq", "GSM1695522", null, "1", "Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.", "GEO Accession:GSM1695522", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP058706", null, null, "zebrafish_RPE_T1.fq.gz", "fastq", 805113700.0, 16102274.0, "GSM1695522 r1", "0:50", "A:218678280;C:181598232;G:182588099;T:221957441;N:291648", 50, null, null, null, 218678280, 181598232, 182588099, 221957441, 291648, "SRX1038068", "SRS945236", "SRA269915", "GEO", "Washington University School of Medicine", 1, 0.86363, null, 0.25795, null, 0.7334, null, 0.5942, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-05-26", "Undetermined", "Undetermined", "Eye", "Sensory System"], [40219, "SRR3143916", "SRX1474053", "SRS1200114", "SRP067229", "PRJNA305621", "Modulation of tissue repair by regeneration enhancer elements.", "GSE75894", "Other", "We compared transcriptional and chromatin profiles of regenerating zebrafish hearts following genetic ablation with profiles from uninjured zebrafish hearts. Overall design: Examination of whole heart transcriptional profiles from ablated hearts 2 pools of 10 hearts and uninjured hearts 2 pools of 10 hearts. Examination of differential H3K27Ac marks following genetic ablation of cardiomyocytes regenerating hearts and uninjured hearts.", null, "pubmed:27049946", null, "ZF Uninjured Hearts 2 PG 2", "GSM1969523", null, "tissue:Whole uninjured hearts|strain:EK/AB|line:gbactin2:loxP mCherry STOP loxP DTA176; cmlc2:CreER|treatment:Propylene glycol", "ZF Uninjured Hearts 2 PG 2", "Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: \"Reads cpms.txt\" is tab delimited text file.  CPMs were calculated using edgeR. Supplementary files format and content: \"Raw read counts.txt\" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.", "Whole uninjured hearts", "Animals were treated with Tamoxifen of propylene glycol", "Hearts were collected 7 days post treatment.  10 ventricles were dissected  rinsed in heparin  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries", null, "strain:EK/AB|line:gbactin2:loxP mCherry STOP loxP DTA176; cmlc2:CreER|treatment:Propylene glycol", "GSM1969523", "GSM1969523: ZF Uninjured Hearts 2 PG 2; Danio rerio; RNA Seq", "GSM1969523", null, "1", "Hearts were collected 7 days post treatment.  10 ventricles were dissected  rinsed in heparin  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries", "GEO Accession:GSM1969523", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP067229", null, null, "PG2_TGACCA_L005_R1.gz", "fastq", 2681585050.0, 53631701.0, "GSM1969523 r11", "0:50", "A:725724149;C:626158732;G:607690303;T:721904776;N:107090", 50, null, null, null, 725724149, 626158732, 607690303, 721904776, 107090, "SRX1474053", "SRS1200114", "SRA316081", "GEO", "Poss, Cell Biology, Duke", 1, 0.9015, null, 0.07041, null, 0.7625, null, 0.50968, null, 50, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-12-10", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [40220, "SRR3143899", "SRX1474052", "SRS1200115", "SRP067229", "PRJNA305621", "Modulation of tissue repair by regeneration enhancer elements.", "GSE75894", "Other", "We compared transcriptional and chromatin profiles of regenerating zebrafish hearts following genetic ablation with profiles from uninjured zebrafish hearts. Overall design: Examination of whole heart transcriptional profiles from ablated hearts 2 pools of 10 hearts and uninjured hearts 2 pools of 10 hearts. Examination of differential H3K27Ac marks following genetic ablation of cardiomyocytes regenerating hearts and uninjured hearts.", null, "pubmed:27049946", null, "ZF Uninjured Hearts 1 PG 1", "GSM1969522", null, "tissue:Whole uninjured hearts|strain:EK/AB|line:gbactin2:loxP mCherry STOP loxP DTA176; cmlc2:CreER|treatment:Propylene glycol", "ZF Uninjured Hearts 1 PG 1", "Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: \"Reads cpms.txt\" is tab delimited text file.  CPMs were calculated using edgeR. Supplementary files format and content: \"Raw read counts.txt\" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.", "Whole uninjured hearts", "Animals were treated with Tamoxifen of propylene glycol", "Hearts were collected 7 days post treatment.  10 ventricles were dissected  rinsed in heparin  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries", null, "strain:EK/AB|line:gbactin2:loxP mCherry STOP loxP DTA176; cmlc2:CreER|treatment:Propylene glycol", "GSM1969522", "GSM1969522: ZF Uninjured Hearts 1 PG 1; Danio rerio; RNA Seq", "GSM1969522", null, "1", "Hearts were collected 7 days post treatment.  10 ventricles were dissected  rinsed in heparin  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries", "GEO Accession:GSM1969522", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP067229", null, null, "PG1_CGATGT_L005_R1.gz", "fastq", 2488196150.0, 49763923.0, "GSM1969522 r11", "0:50", "A:665282679;C:588643091;G:571791112;T:662380843;N:98425", 50, null, null, null, 665282679, 588643091, 571791112, 662380843, 98425, "SRX1474052", "SRS1200115", "SRA316081", "GEO", "Poss, Cell Biology, Duke", 1, 0.91067, null, 0.07205, null, 0.74864, null, 0.496, null, 50, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-12-10", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [40221, "SRR3143897", "SRX1474051", "SRS1200116", "SRP067229", "PRJNA305621", "Modulation of tissue repair by regeneration enhancer elements.", "GSE75894", "Other", "We compared transcriptional and chromatin profiles of regenerating zebrafish hearts following genetic ablation with profiles from uninjured zebrafish hearts. Overall design: Examination of whole heart transcriptional profiles from ablated hearts 2 pools of 10 hearts and uninjured hearts 2 pools of 10 hearts. Examination of differential H3K27Ac marks following genetic ablation of cardiomyocytes regenerating hearts and uninjured hearts.", null, "pubmed:27049946", null, "ZF Ablated Hearts 2 TAM 2", "GSM1969521", null, "tissue:Whole hearts 7d post ablation|strain:EK/AB|line:gbactin2:loxP mCherry STOP loxP DTA176; cmlc2:CreER|treatment:Tamoxifen", "ZF Ablated Hearts 2 TAM 2", "Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: \"Reads cpms.txt\" is tab delimited text file.  CPMs were calculated using edgeR. Supplementary files format and content: \"Raw read counts.txt\" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.", "Whole hearts 7d post ablation", "Animals were treated with Tamoxifen of propylene glycol", "Hearts were collected 7 days post treatment.  10 ventricles were dissected  rinsed in heparin  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries", null, "strain:EK/AB|line:gbactin2:loxP mCherry STOP loxP DTA176; cmlc2:CreER|treatment:Tamoxifen", "GSM1969521", "GSM1969521: ZF Ablated Hearts 2 TAM 2; Danio rerio; RNA Seq", "GSM1969521", null, "1", "Hearts were collected 7 days post treatment.  10 ventricles were dissected  rinsed in heparin  placed in Trizol and homogenized.  RNA was then extracted. Illumina RNA Seq  50 bp Single end libraries", "GEO Accession:GSM1969521", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP067229", null, null, "TAM2_CCGTCC_L005_R1.gz", "fastq", 2751574250.0, 55031485.0, "GSM1969521 r11", "0:50", "A:748951871;C:632985067;G:617593198;T:751936222;N:107892", 50, null, null, null, 748951871, 632985067, 617593198, 751936222, 107892, "SRX1474051", "SRS1200116", "SRA316081", "GEO", "Poss, Cell Biology, Duke", 1, 0.90799, null, 0.09785, null, 0.72799, null, 0.49426, null, 50, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-12-10", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [40222, "SRR3143894", "SRX1474050", "SRS1200117", "SRP067229", "PRJNA305621", "Modulation of tissue repair by regeneration enhancer elements.", "GSE75894", "Other", "We compared transcriptional and chromatin profiles of regenerating zebrafish hearts following genetic ablation with profiles from uninjured zebrafish hearts. 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