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We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.", null, null, null, "muscle sample from 7 mpf zebrafish replicate3", "SAMD00152491", null, "sample name:m07 3|age:7 month|biological replicate:3|tissue:muscle", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152491", "DRX153162", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152491", null, null, null, 1081187000.0, 5405935.0, "DRR162543", "0:100 1:100", "A:272702030;C:267625388;G:270437426;T:268730517;N:1691639", 100, 100, null, null, 272702030, 267625388, 270437426, 268730517, 1691639, "DRX153162", "DRS083223", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.97471, 0.93399, 0.02247, 0.02056, 0.86876, 0.87519, 0.54092, 0.53031, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Adult", "Adult", "Muscle", "Muscular System"], [199, "DRR162542", "DRX153161", "DRS083222", "DRP004696", "PRJDB7713", "Age associated transcriptome analysis in 5 tissues of zebrafish", "DRP004696", "Transcriptome Analysis", "We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. 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We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.", null, null, null, "muscle sample from 7 mpf zebrafish replicate1", "SAMD00152489", null, "sample name:m07 1|age:7 month|biological replicate:1|tissue:muscle", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152489", "DRX153160", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152489", null, null, null, 1331668400.0, 6658342.0, "DRR162541", "0:100 1:100", "A:339618846;C:325463872;G:328670370;T:335855545;N:2059767", 100, 100, null, null, 339618846, 325463872, 328670370, 335855545, 2059767, "DRX153160", "DRS083221", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.9743, 0.93669, 0.02259, 0.02116, 0.84676, 0.85476, 0.54434, 0.53825, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Adult", "Adult", "Muscle", "Muscular System"], [201, "DRR162540", "DRX153159", "DRS083220", "DRP004696", "PRJDB7713", "Age associated transcriptome analysis in 5 tissues of zebrafish", "DRP004696", "Transcriptome Analysis", "We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.", null, null, null, "muscle sample from 2 mpf zebrafish replicate5", "SAMD00152488", null, "sample name:m02 5|age:2 month|biological replicate:5|tissue:muscle", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152488", "DRX153159", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152488", null, null, null, 1063436200.0, 5317181.0, "DRR162540", "0:100 1:100", "A:275438061;C:255805442;G:257091950;T:273487067;N:1613680", 100, 100, null, null, 275438061, 255805442, 257091950, 273487067, 1613680, "DRX153159", "DRS083220", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.96295, 0.92896, 0.04409, 0.0427, 0.75355, 0.76499, 0.49339, 0.50418, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [202, "DRR162539", "DRX153158", "DRS083219", "DRP004696", "PRJDB7713", "Age associated transcriptome analysis in 5 tissues of zebrafish", "DRP004696", "Transcriptome Analysis", "We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.", null, null, null, "muscle sample from 2 mpf zebrafish replicate4", "SAMD00152487", null, "sample name:m02 4|age:2 month|biological replicate:4|tissue:muscle", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152487", "DRX153158", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152487", null, null, null, 1233640200.0, 6168201.0, "DRR162539", "0:100 1:100", "A:318959646;C:297211942;G:300002324;T:315647570;N:1818718", 100, 100, null, null, 318959646, 297211942, 300002324, 315647570, 1818718, "DRX153158", "DRS083219", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.96511, 0.92512, 0.04175, 0.04058, 0.77607, 0.78835, 0.48689, 0.50535, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [203, "DRR162538", "DRX153157", "DRS083218", "DRP004696", "PRJDB7713", "Age associated transcriptome analysis in 5 tissues of zebrafish", "DRP004696", "Transcriptome Analysis", "We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.", null, null, null, "muscle sample from 2 mpf zebrafish replicate3", "SAMD00152486", null, "sample name:m02 3|age:2 month|biological replicate:3|tissue:muscle", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152486", "DRX153157", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152486", null, null, null, 675957200.0, 3379786.0, "DRR162538", "0:100 1:100", "A:173033870;C:164578076;G:165481544;T:171780353;N:1083357", 100, 100, null, null, 173033870, 164578076, 165481544, 171780353, 1083357, "DRX153157", "DRS083218", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.97251, 0.94405, 0.03347, 0.03256, 0.82432, 0.83159, 0.55228, 0.47905, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [204, "DRR162537", "DRX153156", "DRS083217", "DRP004696", "PRJDB7713", "Age associated transcriptome analysis in 5 tissues of zebrafish", "DRP004696", "Transcriptome Analysis", "We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.", null, null, null, "muscle sample from 2 mpf zebrafish replicate2", "SAMD00152485", null, "sample name:m02 2|age:2 month|biological replicate:2|tissue:muscle", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152485", "DRX153156", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152485", null, null, null, 1260768000.0, 6303840.0, "DRR162537", "0:100 1:100", "A:319433176;C:310903964;G:312279388;T:316219239;N:1932233", 100, 100, null, null, 319433176, 310903964, 312279388, 316219239, 1932233, "DRX153156", "DRS083217", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.96774, 0.93275, 0.04099, 0.04003, 0.76919, 0.79626, 0.51687, 0.50638, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [205, "DRR162536", "DRX153155", "DRS083216", "DRP004696", "PRJDB7713", "Age associated transcriptome analysis in 5 tissues of zebrafish", "DRP004696", "Transcriptome Analysis", "We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.", null, null, null, "muscle sample from 2 mpf zebrafish replicate1", "SAMD00152484", null, "sample name:m02 1|age:2 month|biological replicate:1|tissue:muscle", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing of SAMD00152484", "DRX153155", "1", "1", "Illumina TruSeq Stranded mRNA HT Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "DRP004696", "Illumina HiSeq 2000 paired end sequencing of SAMD00152484", null, null, null, 1318898400.0, 6594492.0, "DRR162536", "0:100 1:100", "A:337402722;C:321381897;G:323422706;T:334658718;N:2032357", 100, 100, null, null, 337402722, 321381897, 323422706, 334658718, 2032357, "DRX153155", "DRS083216", "DRA007711", "UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology", "Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo", 2, 0.9692, 0.93768, 0.02944, 0.02852, 0.79431, 0.80359, 0.50636, 0.51065, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-12-24", "Juvenile", "Juvenile", "Muscle", "Muscular System"], [26375, "SRR25897903", "SRX21618264", "SRS18790609", "SRP458313", "PRJNA1012699", "Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish", "GSE242251", "Transcriptome Analysis", "LMNA mutations cause laminopathies a group of rare genetic diseases with no known cure only symptomatic treatment and supportive care. In this study we characterized five LMNA mutations LMNAL35P LMNAA539V LMNAW520G LMNAE358K and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior muscle endurance and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.", null, "pubmed:38834813", null, "RNA seq LMNA R453W 3", "GSM7757086", null, "source name:muscle|tissue:muscle|genotype:LMNA R453W|treatment:N1|geo loc name:missing|collection date:missing", "RNA seq LMNA R453W 3", "Raw data qulity contol by fastQC Trimmomatic those that meet the following conditions will be deleted: 1 Base quality <3 from either 3\u2019 or 5\u2019 end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "muscle", null, "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", "We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 \u00b0C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.", "tissue:muscle|genotype:LMNA R453W|treatment:N1", "GSM7757086", "GSM7757086: RNA seq LMNA R453W 3; Danio rerio; RNA Seq", "GSM7757086 r1", "GSM7757086", "1", "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP458313", null, "loader:fastq load.py", "T9M_R_3_2_paired.fq T9M_R_3_1_paired.fq", "fastq fastq", 4869616993.0, 16355391.0, "GSM7757086 r1", "0:148.93 1:148.81", "A:1252653780;C:1163645903;G:1169939131;T:1283327663;N:50516", 148, 148, null, null, 1252653780, 1163645903, 1169939131, 1283327663, 50516, "SRX21618264", "SRS18790609", "SRA1704662", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", 2, 0.91878, 0.92144, 0.02287, 0.02202, 0.7457, 0.74499, 0.47719, 0.47439, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Taiwan", "2023-09-04", "Adult", "Adult", "Muscle", "Muscular System"], [26376, "SRR25897904", "SRX21618263", "SRS18790608", "SRP458313", "PRJNA1012699", "Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish", "GSE242251", "Transcriptome Analysis", "LMNA mutations cause laminopathies a group of rare genetic diseases with no known cure only symptomatic treatment and supportive care. In this study we characterized five LMNA mutations LMNAL35P LMNAA539V LMNAW520G LMNAE358K and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior muscle endurance and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.", null, "pubmed:38834813", null, "RNA seq LMNA R453W 2", "GSM7757085", null, "source name:muscle|tissue:muscle|genotype:LMNA R453W|treatment:N1|geo loc name:missing|collection date:missing", "RNA seq LMNA R453W 2", "Raw data qulity contol by fastQC Trimmomatic those that meet the following conditions will be deleted: 1 Base quality <3 from either 3\u2019 or 5\u2019 end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "muscle", null, "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", "We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 \u00b0C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.", "tissue:muscle|genotype:LMNA R453W|treatment:N1", "GSM7757085", "GSM7757085: RNA seq LMNA R453W 2; Danio rerio; RNA Seq", "GSM7757085 r1", "GSM7757085", "1", "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP458313", null, "loader:fastq load.py", "T9M_R_2_1_paired.fq T9M_R_2_2_paired.fq", "fastq fastq", 5609014914.0, 18915448.0, "GSM7757085 r1", "0:148.41 1:148.12", "A:1288527357;C:1501761141;G:1493621898;T:1325044624;N:59894", 148, 148, null, null, 1288527357, 1501761141, 1493621898, 1325044624, 59894, "SRX21618263", "SRS18790608", "SRA1704662", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", 2, 0.95814, 0.96074, 0.11463, 0.11555, 0.77713, 0.7767, 0.62814, 0.63117, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Taiwan", "2023-09-04", "Adult", "Adult", "Muscle", "Muscular System"], [26377, "SRR25897905", "SRX21618262", "SRS18790607", "SRP458313", "PRJNA1012699", "Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish", "GSE242251", "Transcriptome Analysis", "LMNA mutations cause laminopathies a group of rare genetic diseases with no known cure only symptomatic treatment and supportive care. In this study we characterized five LMNA mutations LMNAL35P LMNAA539V LMNAW520G LMNAE358K and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior muscle endurance and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.", null, "pubmed:38834813", null, "RNA seq LMNA L35P 3", "GSM7757084", null, "source name:muscle|tissue:muscle|genotype:LMNA L35P|treatment:N1|geo loc name:missing|collection date:missing", "RNA seq LMNA L35P 3", "Raw data qulity contol by fastQC Trimmomatic those that meet the following conditions will be deleted: 1 Base quality <3 from either 3\u2019 or 5\u2019 end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "muscle", null, "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", "We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 \u00b0C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.", "tissue:muscle|genotype:LMNA L35P|treatment:N1", "GSM7757084", "GSM7757084: RNA seq LMNA L35P 3; Danio rerio; RNA Seq", "GSM7757084 r1", "GSM7757084", "1", "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP458313", null, "loader:fastq load.py", "T9M_L_3_1_paired.fq T9M_L_3_2_paired.fq", "fastq fastq", 4769512473.0, 16048426.0, "GSM7757084 r1", "0:148.44 1:148.76", "A:1232520200;C:1137981187;G:1146811734;T:1252148485;N:50867", 148, 148, null, null, 1232520200, 1137981187, 1146811734, 1252148485, 50867, "SRX21618262", "SRS18790607", "SRA1704662", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", 2, 0.95126, 0.95371, 0.04556, 0.04517, 0.75205, 0.75083, 0.49205, 0.49278, 54, 112, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Taiwan", "2023-09-04", "Adult", "Adult", "Muscle", "Muscular System"], [26378, "SRR25897906", "SRX21618261", "SRS18790606", "SRP458313", "PRJNA1012699", "Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish", "GSE242251", "Transcriptome Analysis", "LMNA mutations cause laminopathies a group of rare genetic diseases with no known cure only symptomatic treatment and supportive care. In this study we characterized five LMNA mutations LMNAL35P LMNAA539V LMNAW520G LMNAE358K and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior muscle endurance and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.", null, "pubmed:38834813", null, "RNA seq LMNA L35P 2", "GSM7757083", null, "source name:muscle|tissue:muscle|genotype:LMNA L35P|treatment:N1|geo loc name:missing|collection date:missing", "RNA seq LMNA L35P 2", "Raw data qulity contol by fastQC Trimmomatic those that meet the following conditions will be deleted: 1 Base quality <3 from either 3\u2019 or 5\u2019 end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "muscle", null, "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", "We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 \u00b0C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.", "tissue:muscle|genotype:LMNA L35P|treatment:N1", "GSM7757083", "GSM7757083: RNA seq LMNA L35P 2; Danio rerio; RNA Seq", "GSM7757083 r1", "GSM7757083", "1", "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP458313", null, "loader:fastq load.py", "T9M_L_2_1_paired.fq T9M_L_2_2_paired.fq", "fastq fastq", 3918432824.0, 13209622.0, "GSM7757083 r1", "0:148.33 1:148.31", "A:1055586946;C:892801402;G:895757042;T:1074245534;N:41900", 148, 148, null, null, 1055586946, 892801402, 895757042, 1074245534, 41900, "SRX21618261", "SRS18790606", "SRA1704662", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", 2, 0.93802, 0.93862, 0.13654, 0.13491, 0.70609, 0.70483, 0.50253, 0.50539, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Taiwan", "2023-09-04", "Adult", "Adult", "Muscle", "Muscular System"], [26379, "SRR25897907", "SRX21618260", "SRS18790604", "SRP458313", "PRJNA1012699", "Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish", "GSE242251", "Transcriptome Analysis", "LMNA mutations cause laminopathies a group of rare genetic diseases with no known cure only symptomatic treatment and supportive care. In this study we characterized five LMNA mutations LMNAL35P LMNAA539V LMNAW520G LMNAE358K and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior muscle endurance and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.", null, "pubmed:38834813", null, "RNA seq LMNA E358K 3", "GSM7757082", null, "source name:muscle|tissue:muscle|genotype:LMNA E358K|treatment:N1|geo loc name:missing|collection date:missing", "RNA seq LMNA E358K 3", "Raw data qulity contol by fastQC Trimmomatic those that meet the following conditions will be deleted: 1 Base quality <3 from either 3\u2019 or 5\u2019 end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "muscle", null, "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", "We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 \u00b0C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.", "tissue:muscle|genotype:LMNA E358K|treatment:N1", "GSM7757082", "GSM7757082: RNA seq LMNA E358K 3; Danio rerio; RNA Seq", "GSM7757082 r1", "GSM7757082", "1", "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP458313", null, "loader:fastq load.py", "T9M_E_3_1_paired.fq T9M_E_3_2_paired.fq", "fastq fastq", 2965977779.0, 9986265.0, "GSM7757082 r1", "0:148.42 1:148.59", "A:778091521;C:696132224;G:696171619;T:795550067;N:32348", 148, 148, null, null, 778091521, 696132224, 696171619, 795550067, 32348, "SRX21618260", "SRS18790604", "SRA1704662", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", 2, 0.93505, 0.94207, 0.03691, 0.03615, 0.76165, 0.76067, 0.52238, 0.51874, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Taiwan", "2023-09-04", "Adult", "Adult", "Muscle", "Muscular System"], [26380, "SRR25897908", "SRX21618259", "SRS18790605", "SRP458313", "PRJNA1012699", "Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish", "GSE242251", "Transcriptome Analysis", "LMNA mutations cause laminopathies a group of rare genetic diseases with no known cure only symptomatic treatment and supportive care. In this study we characterized five LMNA mutations LMNAL35P LMNAA539V LMNAW520G LMNAE358K and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior muscle endurance and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.", null, "pubmed:38834813", null, "RNA seq LMNA A539V 3", "GSM7757081", null, "source name:muscle|tissue:muscle|genotype:LMNA A539V|treatment:N1|geo loc name:missing|collection date:missing", "RNA seq LMNA A539V 3", "Raw data qulity contol by fastQC Trimmomatic those that meet the following conditions will be deleted: 1 Base quality <3 from either 3\u2019 or 5\u2019 end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "muscle", null, "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", "We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 \u00b0C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.", "tissue:muscle|genotype:LMNA A539V|treatment:N1", "GSM7757081", "GSM7757081: RNA seq LMNA A539V 3; Danio rerio; RNA Seq", "GSM7757081 r1", "GSM7757081", "1", "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP458313", null, "loader:fastq load.py", "T9M_A_3_1_paired.fq T9M_A_3_2_paired.fq", "fastq fastq", 6072897265.0, 20397882.0, "GSM7757081 r1", "0:148.52 1:149.20", "A:1542358988;C:1476134606;G:1476481844;T:1577859108;N:62719", 148, 149, null, null, 1542358988, 1476134606, 1476481844, 1577859108, 62719, "SRX21618259", "SRS18790605", "SRA1704662", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", 2, 0.94916, 0.95378, 0.03578, 0.03486, 0.75868, 0.75836, 0.51302, 0.51448, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Taiwan", "2023-09-04", "Adult", "Adult", "Muscle", "Muscular System"], [26381, "SRR25897909", "SRX21618258", "SRS18790603", "SRP458313", "PRJNA1012699", "Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish", "GSE242251", "Transcriptome Analysis", "LMNA mutations cause laminopathies a group of rare genetic diseases with no known cure only symptomatic treatment and supportive care. In this study we characterized five LMNA mutations LMNAL35P LMNAA539V LMNAW520G LMNAE358K and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior muscle endurance and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.", null, "pubmed:38834813", null, "RNA seq LMNA A539V 2", "GSM7757080", null, "source name:muscle|tissue:muscle|genotype:LMNA A539V|treatment:N1|geo loc name:missing|collection date:missing", "RNA seq LMNA A539V 2", "Raw data qulity contol by fastQC Trimmomatic those that meet the following conditions will be deleted: 1 Base quality <3 from either 3\u2019 or 5\u2019 end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "muscle", null, "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", "We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 \u00b0C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.", "tissue:muscle|genotype:LMNA A539V|treatment:N1", "GSM7757080", "GSM7757080: RNA seq LMNA A539V 2; Danio rerio; RNA Seq", "GSM7757080 r1", "GSM7757080", "1", "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP458313", null, "loader:fastq load.py", "T9M_A_2_1_paired.fq T9M_A_2_2_paired.fq", "fastq fastq", 4391246410.0, 14783214.0, "GSM7757080 r1", "0:148.32 1:148.72", "A:1147509995;C:1034378687;G:1036117282;T:1173191690;N:48756", 148, 148, null, null, 1147509995, 1034378687, 1036117282, 1173191690, 48756, "SRX21618258", "SRS18790603", "SRA1704662", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", 2, 0.92837, 0.93449, 0.03905, 0.03824, 0.76901, 0.76869, 0.52767, 0.51995, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Taiwan", "2023-09-04", "Adult", "Adult", "Muscle", "Muscular System"], [26382, "SRR25897910", "SRX21618257", "SRS18790602", "SRP458313", "PRJNA1012699", "Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish", "GSE242251", "Transcriptome Analysis", "LMNA mutations cause laminopathies a group of rare genetic diseases with no known cure only symptomatic treatment and supportive care. In this study we characterized five LMNA mutations LMNAL35P LMNAA539V LMNAW520G LMNAE358K and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior muscle endurance and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.", null, "pubmed:38834813", null, "RNA seq LMNA A539V 1", "GSM7757079", null, "source name:muscle|tissue:muscle|genotype:LMNA A539V|treatment:N1|geo loc name:missing|collection date:missing", "RNA seq LMNA A539V 1", "Raw data qulity contol by fastQC Trimmomatic those that meet the following conditions will be deleted: 1 Base quality <3 from either 3\u2019 or 5\u2019 end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "muscle", null, "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", "We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 \u00b0C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.", "tissue:muscle|genotype:LMNA A539V|treatment:N1", "GSM7757079", "GSM7757079: RNA seq LMNA A539V 1; Danio rerio; RNA Seq", "GSM7757079 r1", "GSM7757079", "1", "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP458313", null, "loader:fastq load.py", "T9M_A_1_1_paired.fq T9M_A_1_2_paired.fq", "fastq fastq", 5202925541.0, 17505733.0, "GSM7757079 r1", "0:148.28 1:148.93", "A:1362142748;C:1223349314;G:1225245385;T:1392131416;N:56678", 148, 148, null, null, 1362142748, 1223349314, 1225245385, 1392131416, 56678, "SRX21618257", "SRS18790602", "SRA1704662", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", 2, 0.933, 0.9394, 0.02774, 0.02708, 0.76406, 0.76232, 0.52042, 0.51106, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Taiwan", "2023-09-04", "Adult", "Adult", "Muscle", "Muscular System"], [26383, "SRR25897911", "SRX21618256", "SRS18790601", "SRP458313", "PRJNA1012699", "Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish", "GSE242251", "Transcriptome Analysis", "LMNA mutations cause laminopathies a group of rare genetic diseases with no known cure only symptomatic treatment and supportive care. In this study we characterized five LMNA mutations LMNAL35P LMNAA539V LMNAW520G LMNAE358K and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior muscle endurance and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.", null, "pubmed:38834813", null, "RNA seq LMNA WT 3", "GSM7757078", null, "source name:muscle|tissue:muscle|genotype:LMNA WT|treatment:N1|geo loc name:missing|collection date:missing", "RNA seq LMNA WT 3", "Raw data qulity contol by fastQC Trimmomatic those that meet the following conditions will be deleted: 1 Base quality <3 from either 3\u2019 or 5\u2019 end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "muscle", null, "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", "We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 \u00b0C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.", "tissue:muscle|genotype:LMNA WT|treatment:N1", "GSM7757078", "GSM7757078: RNA seq LMNA WT 3; Danio rerio; RNA Seq", "GSM7757078 r1", "GSM7757078", "1", "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP458313", null, "loader:fastq load.py", "C9M_WT_3_1_paired.fq C9M_WT_3_2_paired.fq", "fastq fastq", 2628000986.0, 8856042.0, "GSM7757078 r1", "0:148.09 1:148.66", "A:662710830;C:644088161;G:643223497;T:677949643;N:28855", 148, 148, null, null, 662710830, 644088161, 643223497, 677949643, 28855, "SRX21618256", "SRS18790601", "SRA1704662", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", 2, 0.9176, 0.93277, 0.04117, 0.04045, 0.78017, 0.7792, 0.55638, 0.56128, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Taiwan", "2023-09-04", "Adult", "Adult", "Muscle", "Muscular System"], [26384, "SRR25897912", "SRX21618255", "SRS18790600", "SRP458313", "PRJNA1012699", "Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish", "GSE242251", "Transcriptome Analysis", "LMNA mutations cause laminopathies a group of rare genetic diseases with no known cure only symptomatic treatment and supportive care. In this study we characterized five LMNA mutations LMNAL35P LMNAA539V LMNAW520G LMNAE358K and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior muscle endurance and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.", null, "pubmed:38834813", null, "RNA seq LMNA WT 2", "GSM7757077", null, "source name:muscle|tissue:muscle|genotype:LMNA WT|treatment:N1|geo loc name:missing|collection date:missing", "RNA seq LMNA WT 2", "Raw data qulity contol by fastQC Trimmomatic those that meet the following conditions will be deleted: 1 Base quality <3 from either 3\u2019 or 5\u2019 end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "muscle", null, "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", "We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 \u00b0C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.", "tissue:muscle|genotype:LMNA WT|treatment:N1", "GSM7757077", "GSM7757077: RNA seq LMNA WT 2; Danio rerio; RNA Seq", "GSM7757077 r1", "GSM7757077", "1", "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP458313", null, "loader:fastq load.py", "C9M_WT_2_1_paired.fq C9M_WT_2_2_paired.fq", "fastq fastq", 4059488026.0, 13662720.0, "GSM7757077 r1", "0:148.27 1:148.85", "A:1083849299;C:934373691;G:936737794;T:1104483688;N:43554", 148, 148, null, null, 1083849299, 934373691, 936737794, 1104483688, 43554, "SRX21618255", "SRS18790600", "SRA1704662", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", 2, 0.90078, 0.90963, 0.03631, 0.03544, 0.77195, 0.77086, 0.5122, 0.51745, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Taiwan", "2023-09-04", "Adult", "Adult", "Muscle", "Muscular System"], [26385, "SRR25897913", "SRX21618254", "SRS18790599", "SRP458313", "PRJNA1012699", "Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish", "GSE242251", "Transcriptome Analysis", "LMNA mutations cause laminopathies a group of rare genetic diseases with no known cure only symptomatic treatment and supportive care. In this study we characterized five LMNA mutations LMNAL35P LMNAA539V LMNAW520G LMNAE358K and LMNAR453W identified from patients diagnosed with muscular laminopathy in the zebrafish model. Overall design: We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior muscle endurance and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.", null, "pubmed:38834813", null, "RNA seq LMNA WT 1", "GSM7757076", null, "source name:muscle|tissue:muscle|genotype:LMNA WT|treatment:N1|geo loc name:missing|collection date:missing", "RNA seq LMNA WT 1", "Raw data qulity contol by fastQC Trimmomatic those that meet the following conditions will be deleted: 1 Base quality <3 from either 3\u2019 or 5\u2019 end. 2 Sequences from reads once the average quality <15 within the sliding window of 4 bases. 3 Read length <36. Post Trimming quality control read alignmnet by HISAT2 Supplementary files format and content: Differential expression analysis by DESeq2 with biological replicates Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "muscle", null, "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", "We established transgenic fish overexpressing wild type LMNA and each of the five LMNA mutants. The zebrafish used in this study were maintained at the Taiwan Zebrafish Core Facility TZFC which operates under an automatic 14/10 hour light/dark cycle and maintains the water temperature at 28 \u00b0C by using a circulating water system. Adult fish were normally fed twice daily at 10 a.m. and 3 p.m unless specifically mentioned.", "tissue:muscle|genotype:LMNA WT|treatment:N1", "GSM7757076", "GSM7757076: RNA seq LMNA WT 1; Danio rerio; RNA Seq", "GSM7757076 r1", "GSM7757076", "1", "RNA was harvested using NucleoSpin\u00ae RNA kit MACHEREY NAGEL. 5 ug of total RNA was used for the construction of sequencing libraries. TruSeq\u00ae Stranded mRNA Library Prep", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP458313", null, "loader:fastq load.py", "C9M_WT_1_1_paired.fq C9M_WT_1_2_paired.fq", "fastq fastq", 4489983125.0, 15074997.0, "GSM7757076 r1", "0:148.39 1:149.46", "A:1155122223;C:1073285000;G:1078875040;T:1182655637;N:45225", 148, 149, null, null, 1155122223, 1073285000, 1078875040, 1182655637, 45225, "SRX21618254", "SRS18790599", "SRA1704662", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "Institute of Molecular and Genomic Medicine, National Health Research Institutes", 2, 0.91917, 0.92221, 0.02417, 0.02377, 0.75126, 0.7489, 0.48289, 0.48398, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Taiwan", "2023-09-04", "Adult", "Adult", "Muscle", "Muscular System"], [29641, "SRR27397714", "SRX23073965", "SRS20033317", "SRP480899", "PRJNA1060279", "EPIFISH", "PRJNA1060279", "Other", "Epigenetic changes in fish during domestication", null, null, null, "RRBS library10", "PG2", null, "strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 10|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of danio rerio", "RRBS10", "RRBS10", "Library preparation kit used Zymo Seq RRBS Library Kit", null, null, "Bisulfite-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP480899", null, null, "PG2_L7_1.fq.gz PG2_L7_2.fq.gz", "fastq fastq", 981695400.0, 3272318.0, "PG2 L7 1.fq.gz", "0:150 1:150", "A:253124715;C:152724975;G:341105704;T:234698202;N:41804", 150, 150, null, null, 253124715, 152724975, 341105704, 234698202, 41804, "SRX23073965", "SRS20033317", "SRA1777947", "Nord University|Bioscience and Aquaculture", "Nord University", 2, 0.0164, 0.00047, 0.01505, 0.00036, 0.9961, 0.99965, 0.58102, 0.47058, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2024-01-02", "Adult", "Adult", "Muscle", "Muscular System"], [29642, "SRR27397715", "SRX23073964", "SRS20033316", "SRP480899", "PRJNA1060279", "EPIFISH", "PRJNA1060279", "Other", "Epigenetic changes in fish during domestication", null, null, null, "RRBS library9", "PG1", null, "strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 9|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of danio rerio", "RRBS9", "RRBS9", "Library preparation kit used Zymo Seq RRBS Library Kit", null, null, "Bisulfite-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP480899", null, null, "PG1_L7_1.fq.gz PG1_L7_2.fq.gz", "fastq fastq", 1157067600.0, 3856892.0, "PG1 L7 1.fq.gz", "0:150 1:150", "A:278308283;C:162228777;G:432676687;T:283803806;N:50047", 150, 150, null, null, 278308283, 162228777, 432676687, 283803806, 50047, "SRX23073964", "SRS20033316", "SRA1777947", "Nord University|Bioscience and Aquaculture", "Nord University", 2, 0.02347, 0.02319, 0.02188, 0.02162, 0.99517, 0.99519, 0.50342, 0.51027, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2024-01-02", "Adult", "Adult", "Muscle", "Muscular System"], [29643, "SRR27397716", "SRX23073963", "SRS20033315", "SRP480899", "PRJNA1060279", "EPIFISH", "PRJNA1060279", "Other", "Epigenetic changes in fish during domestication", null, null, null, "RRBS library8", "LG4", null, "strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 8|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of danio rerio", "RRBS8", "RRBS8", "Library preparation kit used Zymo Seq RRBS Library Kit", null, null, "Bisulfite-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP480899", null, null, "LG4_L7_1.fq.gz LG4_L7_2.fq.gz", "fastq fastq", 1080684300.0, 3602281.0, "LG4 L7 1.fq.gz", "0:150 1:150", "A:270759422;C:159278390;G:387693215;T:262907381;N:45892", 150, 150, null, null, 270759422, 159278390, 387693215, 262907381, 45892, "SRX23073963", "SRS20033315", "SRA1777947", "Nord University|Bioscience and Aquaculture", "Nord University", 2, 0.01698, 0.00033, 0.01593, 0.00026, 0.99675, 0.99979, 0.4974, 0.2, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2024-01-02", "Adult", "Adult", "Muscle", "Muscular System"], [29644, "SRR27397717", "SRX23073962", "SRS20033314", "SRP480899", "PRJNA1060279", "EPIFISH", "PRJNA1060279", "Other", "Epigenetic changes in fish during domestication", null, null, null, "RRBS library7", "LG3", null, "strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of danio rerio", "RRBS7", "RRBS7", "Library preparation kit used Zymo Seq RRBS Library Kit", null, null, "Bisulfite-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP480899", null, null, "LG3_L7_1.fq.gz LG3_L7_2.fq.gz", "fastq fastq", 1223063700.0, 4076879.0, "LG3 L7 1.fq.gz", "0:150 1:150", "A:301167012;C:182106743;G:443329321;T:296409064;N:51560", 150, 150, null, null, 301167012, 182106743, 443329321, 296409064, 51560, "SRX23073962", "SRS20033314", "SRA1777947", "Nord University|Bioscience and Aquaculture", "Nord University", 2, 0.01787, 0.01759, 0.01644, 0.01622, 0.99545, 0.99582, 0.56826, 0.56126, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2024-01-02", "Adult", "Adult", "Muscle", "Muscular System"], [29645, "SRR27397718", "SRX23073961", "SRS20033313", "SRP480899", "PRJNA1060279", "EPIFISH", "PRJNA1060279", "Other", "Epigenetic changes in fish during domestication", null, null, null, "RRBS library6", "LG2", null, "strain:ab|age:adult|collection date:2023 02 07|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of danio rerio", "RRBS6", "RRBS6", "Library preparation kit used Zymo Seq RRBS Library Kit", null, null, "Bisulfite-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP480899", null, null, "LG2_L7_1.fq.gz LG2_L7_2.fq.gz", "fastq fastq", 1188600300.0, 3962001.0, "LG2 L7 1.fq.gz", "0:150 1:150", "A:294477343;C:172669379;G:418732939;T:302669966;N:50673", 150, 150, null, null, 294477343, 172669379, 418732939, 302669966, 50673, "SRX23073961", "SRS20033313", "SRA1777947", "Nord University|Bioscience and Aquaculture", "Nord University", 2, 0.0205, 0.02042, 0.01903, 0.01894, 0.99584, 0.99577, 0.51685, 0.51824, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2024-01-02", "Adult", "Adult", "Muscle", "Muscular System"], [29646, "SRR27397719", "SRX23073960", "SRS20033312", "SRP480899", "PRJNA1060279", "EPIFISH", "PRJNA1060279", "Other", "Epigenetic changes in fish during domestication", null, null, null, "RRBS library5", "LG1", null, "strain:ab|age:adult|collection date:2023 02 06|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of danio rerio", "RRBS5", "RRBS5", "Library preparation kit used Zymo Seq RRBS Library Kit", null, null, "Bisulfite-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP480899", null, null, "LG1_L7_1.fq.gz LG1_L7_2.fq.gz", "fastq fastq", 1048183200.0, 3493944.0, "LG1 L7 1.fq.gz", "0:150 1:150", "A:260330612;C:163890192;G:372783427;T:251133569;N:45400", 150, 150, null, null, 260330612, 163890192, 372783427, 251133569, 45400, "SRX23073960", "SRS20033312", "SRA1777947", "Nord University|Bioscience and Aquaculture", "Nord University", 2, 0.01999, 0.00059, 0.01851, 0.00045, 0.99563, 0.99961, 0.49816, 0.36842, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2024-01-02", "Adult", "Adult", "Muscle", "Muscular System"], [29647, "SRR27397720", "SRX23073959", "SRS20033311", "SRP480899", "PRJNA1060279", "EPIFISH", "PRJNA1060279", "Other", "Epigenetic changes in fish during domestication", null, null, null, "RRBS library4", "CG4", null, "strain:ab|age:adult|collection date:2023 02 05|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of danio rerio", "RRBS4", "RRBS4", "Library preparation kit used Zymo Seq RRBS Library Kit", null, null, "Bisulfite-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP480899", null, null, "CG4_L7_1.fq.gz CG4_L7_2.fq.gz", "fastq fastq", 1547200200.0, 5157334.0, "CG4 L7 1.fq.gz", "0:150 1:150", "A:389261224;C:230650937;G:559928386;T:367293552;N:66101", 150, 150, null, null, 389261224, 230650937, 559928386, 367293552, 66101, "SRX23073959", "SRS20033311", "SRA1777947", "Nord University|Bioscience and Aquaculture", "Nord University", 2, 0.01121, 0.00022, 0.01024, 0.00018, 0.99713, 0.99991, 0.56111, 1.0, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2024-01-02", "Adult", "Adult", "Muscle", "Muscular System"], [29648, "SRR27397721", "SRX23073958", "SRS20033310", "SRP480899", "PRJNA1060279", "EPIFISH", "PRJNA1060279", "Other", "Epigenetic changes in fish during domestication", null, null, null, "RRBS library3", "CG3", null, "strain:ab|age:adult|collection date:2023 02 04|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of danio rerio", "RRBS3", "RRBS3", "Library preparation kit used Zymo Seq RRBS Library Kit", null, null, "Bisulfite-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP480899", null, null, "CG3_L7_1.fq.gz CG3_L7_2.fq.gz", "fastq fastq", 1164022500.0, 3880075.0, "CG3 L7 1.fq.gz", "0:150 1:150", "A:281490630;C:172929357;G:423757698;T:285795200;N:49615", 150, 150, null, null, 281490630, 172929357, 423757698, 285795200, 49615, "SRX23073958", "SRS20033310", "SRA1777947", "Nord University|Bioscience and Aquaculture", "Nord University", 2, 0.0188, 0.00046, 0.01744, 0.00039, 0.99626, 0.99981, 0.55421, 0.6, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2024-01-02", "Adult", "Adult", "Muscle", "Muscular System"], [29649, "SRR27397722", "SRX23073957", "SRS20033309", "SRP480899", "PRJNA1060279", "EPIFISH", "PRJNA1060279", "Other", "Epigenetic changes in fish during domestication", null, null, null, "RRBS library12", "PG4", null, "strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 12|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of danio rerio", "RRBS12", "RRBS12", "Library preparation kit used Zymo Seq RRBS Library Kit", null, null, "Bisulfite-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP480899", null, null, "PG4_L7_1.fq.gz PG4_L7_2.fq.gz", "fastq fastq", 937521000.0, 3125070.0, "PG4 L7 1.fq.gz", "0:150 1:150", "A:230277419;C:145742183;G:328432893;T:233027715;N:40790", 150, 150, null, null, 230277419, 145742183, 328432893, 233027715, 40790, "SRX23073957", "SRS20033309", "SRA1777947", "Nord University|Bioscience and Aquaculture", "Nord University", 2, 0.01943, 0.01926, 0.01799, 0.01786, 0.99575, 0.99588, 0.51136, 0.48062, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2024-01-02", "Adult", "Adult", "Muscle", "Muscular System"], [29650, "SRR27397723", "SRX23073956", "SRS20033308", "SRP480899", "PRJNA1060279", "EPIFISH", "PRJNA1060279", "Other", "Epigenetic changes in fish during domestication", null, null, null, "RRBS library11", "PG3", null, "strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 11|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of danio rerio", "RRBS11", "RRBS11", "Library preparation kit used Zymo Seq RRBS Library Kit", null, null, "Bisulfite-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP480899", null, null, "PG3_L7_1.fq.gz PG3_L7_2.fq.gz", "fastq fastq", 1256812500.0, 4189375.0, "PG3 L7 1.fq.gz", "0:150 1:150", "A:318736087;C:194540494;G:434374337;T:309107761;N:53821", 150, 150, null, null, 318736087, 194540494, 434374337, 309107761, 53821, "SRX23073956", "SRS20033308", "SRA1777947", "Nord University|Bioscience and Aquaculture", "Nord University", 2, 0.01424, 0.00046, 0.01316, 0.00036, 0.99683, 0.99975, 0.49746, 0.5, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2024-01-02", "Adult", "Adult", "Muscle", "Muscular System"], [29651, "SRR27397724", "SRX23073955", "SRS20033307", "SRP480899", "PRJNA1060279", "EPIFISH", "PRJNA1060279", "Other", "Epigenetic changes in fish during domestication", null, null, null, "RRBS library2", "CG2", null, "strain:ab|age:adult|collection date:2023 02 03|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of danio rerio", "RRBS2", "RRBS2", "Library preparation kit used Zymo Seq RRBS Library Kit", null, null, "Bisulfite-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP480899", null, null, "CG2_L7_1.fq.gz CG2_L7_2.fq.gz", "fastq fastq", 1157888400.0, 3859628.0, "CG2 L7 1.fq.gz", "0:150 1:150", "A:292628434;C:171796176;G:406707172;T:286706357;N:50261", 150, 150, null, null, 292628434, 171796176, 406707172, 286706357, 50261, "SRX23073955", "SRS20033307", "SRA1777947", "Nord University|Bioscience and Aquaculture", "Nord University", 2, 0.02036, 0.02023, 0.01903, 0.01889, 0.99616, 0.99614, 0.55102, 0.57894, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2024-01-02", "Adult", "Adult", "Muscle", "Muscular System"], [29652, "SRR27397725", "SRX23073954", "SRS20033306", "SRP480899", "PRJNA1060279", "EPIFISH", "PRJNA1060279", "Other", "Epigenetic changes in fish during domestication", null, null, null, "RRBS library1", "CG1", null, "strain:ab|age:adult|collection date:2023 02 02|geo loc name:Italy|sex:male|tissue:Muscle|Source materail identifiers:day 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of danio rerio", "RRBS1", "RRBS1", "Library preparation kit used Zymo Seq RRBS Library Kit", null, null, "Bisulfite-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP480899", null, null, "CG1_L7_1.fq.gz CG1_L7_2.fq.gz", "fastq fastq", 1004867700.0, 3349559.0, "CG1 L7 1.fq.gz", "0:150 1:150", "A:247727849;C:158203386;G:350367173;T:248526527;N:42765", 150, 150, null, null, 247727849, 158203386, 350367173, 248526527, 42765, "SRX23073954", "SRS20033306", "SRA1777947", "Nord University|Bioscience and Aquaculture", "Nord University", 2, 0.02764, 0.00147, 0.0252, 0.00121, 0.99233, 0.99926, 0.51541, 0.5, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2024-01-02", "Adult", "Adult", "Muscle", "Muscular System"], [33817, "SRR30712573", "SRX26116362", "SRS22679901", "SRP533374", "PRJNA1162497", "Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish", "GSE277480", "Transcriptome Analysis", "The ANKRD1 gene is responsive to different forms of mechanical stress including injury stretching resistance exercise and eccentric contractions. We showed that ankrd1a zebrafish homologue of mammalian ANKRD1 gets activated in the heart post cryoinjury of the ventricle and in skeletal muscle post stab wound suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction muscle cell differentiation MAPK and integrin mediated signaling pathways and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery RNA was isolated from the muscle tissue around the injury anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt non injured wt injured mutant and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.", null, null, null, "mut I 4", "GSM8523061", null, "source name:skeletal muscle|tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:injured|geo loc name:missing|collection date:missing", "mut I 4", "fastp v0.23.4 STAR v2.7.0 RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20 nqualified percent limit=30 average qual=25 low complexity filter=True complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110 Ensembl v110 using STAR v2.7.10 with standard parameters except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3 to estimate transcript and gene abundances. Subsequently the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110 Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample", "skeletal muscle", "Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail in line with the anal opening. Immediately post the injury fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle just behind the anal opening and containing the injury area anterior and posterior to the needle lesion was dissected by a razor blade and used for RNA isolation.", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", "Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions in circulating water system under 14 h light/10 h dark cycle and at 28.5 \u25e6C.", "tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:injured", "GSM8523061", "GSM8523061: mut I 4; Danio rerio; RNA Seq", "GSM8523061 r1", "GSM8523061", "1", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP533374", null, null, "1525069_S34_R1_001.fastq.gz 1525069_S34_R2_001.fastq.gz", "fastq fastq", 6968777444.0, 23075422.0, "GSM8523061 r1", "0:151 1:151", "A:1784361774;C:1727895848;G:1635536759;T:1820585862;N:397201", 151, 151, null, null, 1784361774, 1727895848, 1635536759, 1820585862, 397201, "SRX26116362", "SRS22679901", "SRA2089519", "Institute of Molecular Genetic and Genetic Engineering", "Institute of Molecular Genetic and Genetic Engineering", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Serbia", "2024-09-18", "Adult", "Adult", "Muscle", "Muscular System"], [33818, "SRR30712574", "SRX26116361", "SRS22679900", "SRP533374", "PRJNA1162497", "Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish", "GSE277480", "Transcriptome Analysis", "The ANKRD1 gene is responsive to different forms of mechanical stress including injury stretching resistance exercise and eccentric contractions. We showed that ankrd1a zebrafish homologue of mammalian ANKRD1 gets activated in the heart post cryoinjury of the ventricle and in skeletal muscle post stab wound suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction muscle cell differentiation MAPK and integrin mediated signaling pathways and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery RNA was isolated from the muscle tissue around the injury anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt non injured wt injured mutant and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.", null, null, null, "mut I 3", "GSM8523060", null, "source name:skeletal muscle|tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:injured|geo loc name:missing|collection date:missing", "mut I 3", "fastp v0.23.4 STAR v2.7.0 RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20 nqualified percent limit=30 average qual=25 low complexity filter=True complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110 Ensembl v110 using STAR v2.7.10 with standard parameters except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3 to estimate transcript and gene abundances. Subsequently the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110 Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample", "skeletal muscle", "Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail in line with the anal opening. Immediately post the injury fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle just behind the anal opening and containing the injury area anterior and posterior to the needle lesion was dissected by a razor blade and used for RNA isolation.", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", "Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions in circulating water system under 14 h light/10 h dark cycle and at 28.5 \u25e6C.", "tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:injured", "GSM8523060", "GSM8523060: mut I 3; Danio rerio; RNA Seq", "GSM8523060 r1", "GSM8523060", "1", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP533374", null, null, "1525068_S33_R1_001.fastq.gz 1525068_S33_R2_001.fastq.gz", "fastq fastq", 6689942656.0, 22152128.0, "GSM8523060 r1", "0:151 1:151", "A:1712641463;C:1649736138;G:1564669718;T:1762517154;N:378183", 151, 151, null, null, 1712641463, 1649736138, 1564669718, 1762517154, 378183, "SRX26116361", "SRS22679900", "SRA2089519", "Institute of Molecular Genetic and Genetic Engineering", "Institute of Molecular Genetic and Genetic Engineering", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Serbia", "2024-09-18", "Adult", "Adult", "Muscle", "Muscular System"], [33819, "SRR30712575", "SRX26116360", "SRS22679899", "SRP533374", "PRJNA1162497", "Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish", "GSE277480", "Transcriptome Analysis", "The ANKRD1 gene is responsive to different forms of mechanical stress including injury stretching resistance exercise and eccentric contractions. We showed that ankrd1a zebrafish homologue of mammalian ANKRD1 gets activated in the heart post cryoinjury of the ventricle and in skeletal muscle post stab wound suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction muscle cell differentiation MAPK and integrin mediated signaling pathways and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery RNA was isolated from the muscle tissue around the injury anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt non injured wt injured mutant and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.", null, null, null, "mut I 2", "GSM8523059", null, "source name:skeletal muscle|tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:injured|geo loc name:missing|collection date:missing", "mut I 2", "fastp v0.23.4 STAR v2.7.0 RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20 nqualified percent limit=30 average qual=25 low complexity filter=True complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110 Ensembl v110 using STAR v2.7.10 with standard parameters except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3 to estimate transcript and gene abundances. Subsequently the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110 Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample", "skeletal muscle", "Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail in line with the anal opening. Immediately post the injury fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle just behind the anal opening and containing the injury area anterior and posterior to the needle lesion was dissected by a razor blade and used for RNA isolation.", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", "Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions in circulating water system under 14 h light/10 h dark cycle and at 28.5 \u25e6C.", "tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:injured", "GSM8523059", "GSM8523059: mut I 2; Danio rerio; RNA Seq", "GSM8523059 r1", "GSM8523059", "1", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP533374", null, null, "1525067_S32_R1_001.fastq.gz 1525067_S32_R2_001.fastq.gz", "fastq fastq", 6838079394.0, 22642647.0, "GSM8523059 r1", "0:151 1:151", "A:1753283488;C:1683533113;G:1593714937;T:1807162545;N:385311", 151, 151, null, null, 1753283488, 1683533113, 1593714937, 1807162545, 385311, "SRX26116360", "SRS22679899", "SRA2089519", "Institute of Molecular Genetic and Genetic Engineering", "Institute of Molecular Genetic and Genetic Engineering", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Serbia", "2024-09-18", "Adult", "Adult", "Muscle", "Muscular System"], [33820, "SRR30712576", "SRX26116359", "SRS22679898", "SRP533374", "PRJNA1162497", "Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish", "GSE277480", "Transcriptome Analysis", "The ANKRD1 gene is responsive to different forms of mechanical stress including injury stretching resistance exercise and eccentric contractions. We showed that ankrd1a zebrafish homologue of mammalian ANKRD1 gets activated in the heart post cryoinjury of the ventricle and in skeletal muscle post stab wound suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction muscle cell differentiation MAPK and integrin mediated signaling pathways and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery RNA was isolated from the muscle tissue around the injury anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt non injured wt injured mutant and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.", null, null, null, "mut I 1", "GSM8523058", null, "source name:skeletal muscle|tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:injured|geo loc name:missing|collection date:missing", "mut I 1", "fastp v0.23.4 STAR v2.7.0 RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20 nqualified percent limit=30 average qual=25 low complexity filter=True complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110 Ensembl v110 using STAR v2.7.10 with standard parameters except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3 to estimate transcript and gene abundances. Subsequently the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110 Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample", "skeletal muscle", "Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail in line with the anal opening. Immediately post the injury fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle just behind the anal opening and containing the injury area anterior and posterior to the needle lesion was dissected by a razor blade and used for RNA isolation.", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", "Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions in circulating water system under 14 h light/10 h dark cycle and at 28.5 \u25e6C.", "tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:injured", "GSM8523058", "GSM8523058: mut I 1; Danio rerio; RNA Seq", "GSM8523058 r1", "GSM8523058", "1", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP533374", null, null, "1525066_S31_R1_001.fastq.gz 1525066_S31_R2_001.fastq.gz", "fastq fastq", 6913447118.0, 22892209.0, "GSM8523058 r1", "0:151 1:151", "A:1777855775;C:1703268831;G:1606126723;T:1825808576;N:387213", 151, 151, null, null, 1777855775, 1703268831, 1606126723, 1825808576, 387213, "SRX26116359", "SRS22679898", "SRA2089519", "Institute of Molecular Genetic and Genetic Engineering", "Institute of Molecular Genetic and Genetic Engineering", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Serbia", "2024-09-18", "Adult", "Adult", "Muscle", "Muscular System"], [33821, "SRR30712577", "SRX26116358", "SRS22679897", "SRP533374", "PRJNA1162497", "Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish", "GSE277480", "Transcriptome Analysis", "The ANKRD1 gene is responsive to different forms of mechanical stress including injury stretching resistance exercise and eccentric contractions. We showed that ankrd1a zebrafish homologue of mammalian ANKRD1 gets activated in the heart post cryoinjury of the ventricle and in skeletal muscle post stab wound suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction muscle cell differentiation MAPK and integrin mediated signaling pathways and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery RNA was isolated from the muscle tissue around the injury anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt non injured wt injured mutant and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.", null, null, null, "mut NI 4", "GSM8523057", null, "source name:skeletal muscle|tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:non injured|geo loc name:missing|collection date:missing", "mut NI 4", "fastp v0.23.4 STAR v2.7.0 RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20 nqualified percent limit=30 average qual=25 low complexity filter=True complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110 Ensembl v110 using STAR v2.7.10 with standard parameters except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3 to estimate transcript and gene abundances. Subsequently the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110 Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample", "skeletal muscle", "Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail in line with the anal opening. Immediately post the injury fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle just behind the anal opening and containing the injury area anterior and posterior to the needle lesion was dissected by a razor blade and used for RNA isolation.", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", "Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions in circulating water system under 14 h light/10 h dark cycle and at 28.5 \u25e6C.", "tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:non injured", "GSM8523057", "GSM8523057: mut NI 4; Danio rerio; RNA Seq", "GSM8523057 r1", "GSM8523057", "1", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP533374", null, null, "1525065_S30_R1_001.fastq.gz 1525065_S30_R2_001.fastq.gz", "fastq fastq", 7146614372.0, 23664286.0, "GSM8523057 r1", "0:151 1:151", "A:1820135371;C:1776367719;G:1681029667;T:1868675511;N:406104", 151, 151, null, null, 1820135371, 1776367719, 1681029667, 1868675511, 406104, "SRX26116358", "SRS22679897", "SRA2089519", "Institute of Molecular Genetic and Genetic Engineering", "Institute of Molecular Genetic and Genetic Engineering", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Serbia", "2024-09-18", "Adult", "Adult", "Muscle", "Muscular System"], [33822, "SRR30712578", "SRX26116357", "SRS22679896", "SRP533374", "PRJNA1162497", "Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish", "GSE277480", "Transcriptome Analysis", "The ANKRD1 gene is responsive to different forms of mechanical stress including injury stretching resistance exercise and eccentric contractions. We showed that ankrd1a zebrafish homologue of mammalian ANKRD1 gets activated in the heart post cryoinjury of the ventricle and in skeletal muscle post stab wound suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction muscle cell differentiation MAPK and integrin mediated signaling pathways and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery RNA was isolated from the muscle tissue around the injury anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt non injured wt injured mutant and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.", null, null, null, "mut NI 3", "GSM8523056", null, "source name:skeletal muscle|tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:non injured|geo loc name:missing|collection date:missing", "mut NI 3", "fastp v0.23.4 STAR v2.7.0 RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20 nqualified percent limit=30 average qual=25 low complexity filter=True complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110 Ensembl v110 using STAR v2.7.10 with standard parameters except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3 to estimate transcript and gene abundances. Subsequently the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110 Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample", "skeletal muscle", "Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail in line with the anal opening. Immediately post the injury fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle just behind the anal opening and containing the injury area anterior and posterior to the needle lesion was dissected by a razor blade and used for RNA isolation.", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", "Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions in circulating water system under 14 h light/10 h dark cycle and at 28.5 \u25e6C.", "tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:non injured", "GSM8523056", "GSM8523056: mut NI 3; Danio rerio; RNA Seq", "GSM8523056 r1", "GSM8523056", "1", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP533374", null, null, "1525064_S29_R1_001.fastq.gz 1525064_S29_R2_001.fastq.gz", "fastq fastq", 7041561558.0, 23316429.0, "GSM8523056 r1", "0:151 1:151", "A:1817821542;C:1726630082;G:1641523411;T:1855187749;N:398774", 151, 151, null, null, 1817821542, 1726630082, 1641523411, 1855187749, 398774, "SRX26116357", "SRS22679896", "SRA2089519", "Institute of Molecular Genetic and Genetic Engineering", "Institute of Molecular Genetic and Genetic Engineering", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Serbia", "2024-09-18", "Adult", "Adult", "Muscle", "Muscular System"], [33823, "SRR30712579", "SRX26116356", "SRS22679895", "SRP533374", "PRJNA1162497", "Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish", "GSE277480", "Transcriptome Analysis", "The ANKRD1 gene is responsive to different forms of mechanical stress including injury stretching resistance exercise and eccentric contractions. We showed that ankrd1a zebrafish homologue of mammalian ANKRD1 gets activated in the heart post cryoinjury of the ventricle and in skeletal muscle post stab wound suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction muscle cell differentiation MAPK and integrin mediated signaling pathways and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery RNA was isolated from the muscle tissue around the injury anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt non injured wt injured mutant and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.", null, null, null, "mut NI 2", "GSM8523055", null, "source name:skeletal muscle|tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:non injured|geo loc name:missing|collection date:missing", "mut NI 2", "fastp v0.23.4 STAR v2.7.0 RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20 nqualified percent limit=30 average qual=25 low complexity filter=True complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110 Ensembl v110 using STAR v2.7.10 with standard parameters except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3 to estimate transcript and gene abundances. Subsequently the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110 Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample", "skeletal muscle", "Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail in line with the anal opening. Immediately post the injury fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle just behind the anal opening and containing the injury area anterior and posterior to the needle lesion was dissected by a razor blade and used for RNA isolation.", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", "Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions in circulating water system under 14 h light/10 h dark cycle and at 28.5 \u25e6C.", "tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:non injured", "GSM8523055", "GSM8523055: mut NI 2; Danio rerio; RNA Seq", "GSM8523055 r1", "GSM8523055", "1", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP533374", null, null, "1525063_S28_R1_001.fastq.gz 1525063_S28_R2_001.fastq.gz", "fastq fastq", 6855229974.0, 22699437.0, "GSM8523055 r1", "0:151 1:151", "A:1773305175;C:1678771882;G:1578466224;T:1824300431;N:386262", 151, 151, null, null, 1773305175, 1678771882, 1578466224, 1824300431, 386262, "SRX26116356", "SRS22679895", "SRA2089519", "Institute of Molecular Genetic and Genetic Engineering", "Institute of Molecular Genetic and Genetic Engineering", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Serbia", "2024-09-18", "Adult", "Adult", "Muscle", "Muscular System"], [33824, "SRR30712580", "SRX26116355", "SRS22679894", "SRP533374", "PRJNA1162497", "Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish", "GSE277480", "Transcriptome Analysis", "The ANKRD1 gene is responsive to different forms of mechanical stress including injury stretching resistance exercise and eccentric contractions. We showed that ankrd1a zebrafish homologue of mammalian ANKRD1 gets activated in the heart post cryoinjury of the ventricle and in skeletal muscle post stab wound suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction muscle cell differentiation MAPK and integrin mediated signaling pathways and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery RNA was isolated from the muscle tissue around the injury anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt non injured wt injured mutant and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.", null, null, null, "mut NI 1", "GSM8523054", null, "source name:skeletal muscle|tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:non injured|geo loc name:missing|collection date:missing", "mut NI 1", "fastp v0.23.4 STAR v2.7.0 RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20 nqualified percent limit=30 average qual=25 low complexity filter=True complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110 Ensembl v110 using STAR v2.7.10 with standard parameters except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3 to estimate transcript and gene abundances. Subsequently the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110 Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample", "skeletal muscle", "Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail in line with the anal opening. Immediately post the injury fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle just behind the anal opening and containing the injury area anterior and posterior to the needle lesion was dissected by a razor blade and used for RNA isolation.", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", "Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions in circulating water system under 14 h light/10 h dark cycle and at 28.5 \u25e6C.", "tissue:skeletal muscle|genotype:ankrd1a mutant|treatment:non injured", "GSM8523054", "GSM8523054: mut NI 1; Danio rerio; RNA Seq", "GSM8523054 r1", "GSM8523054", "1", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP533374", null, null, "1525062_S27_R1_001.fastq.gz 1525062_S27_R2_001.fastq.gz", "fastq fastq", 7650351278.0, 25332289.0, "GSM8523054 r1", "0:151 1:151", "A:1981492979;C:1869766013;G:1772110806;T:2026550473;N:431007", 151, 151, null, null, 1981492979, 1869766013, 1772110806, 2026550473, 431007, "SRX26116355", "SRS22679894", "SRA2089519", "Institute of Molecular Genetic and Genetic Engineering", "Institute of Molecular Genetic and Genetic Engineering", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Serbia", "2024-09-18", "Adult", "Adult", "Muscle", "Muscular System"], [33825, "SRR30712581", "SRX26116354", "SRS22679893", "SRP533374", "PRJNA1162497", "Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish", "GSE277480", "Transcriptome Analysis", "The ANKRD1 gene is responsive to different forms of mechanical stress including injury stretching resistance exercise and eccentric contractions. We showed that ankrd1a zebrafish homologue of mammalian ANKRD1 gets activated in the heart post cryoinjury of the ventricle and in skeletal muscle post stab wound suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction muscle cell differentiation MAPK and integrin mediated signaling pathways and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery RNA was isolated from the muscle tissue around the injury anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt non injured wt injured mutant and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.", null, null, null, "wt I 4", "GSM8523053", null, "source name:skeletal muscle|tissue:skeletal muscle|genotype:wt|treatment:injured|geo loc name:missing|collection date:missing", "wt I 4", "fastp v0.23.4 STAR v2.7.0 RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20 nqualified percent limit=30 average qual=25 low complexity filter=True complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110 Ensembl v110 using STAR v2.7.10 with standard parameters except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3 to estimate transcript and gene abundances. Subsequently the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110 Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample", "skeletal muscle", "Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail in line with the anal opening. Immediately post the injury fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle just behind the anal opening and containing the injury area anterior and posterior to the needle lesion was dissected by a razor blade and used for RNA isolation.", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", "Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions in circulating water system under 14 h light/10 h dark cycle and at 28.5 \u25e6C.", "tissue:skeletal muscle|genotype:wt|treatment:injured", "GSM8523053", "GSM8523053: wt I 4; Danio rerio; RNA Seq", "GSM8523053 r1", "GSM8523053", "1", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP533374", null, null, "1525061_S26_R1_001.fastq.gz 1525061_S26_R2_001.fastq.gz", "fastq fastq", 9052754718.0, 29976009.0, "GSM8523053 r1", "0:151 1:151", "A:2314195920;C:2237646210;G:2107364469;T:2393040833;N:507286", 151, 151, null, null, 2314195920, 2237646210, 2107364469, 2393040833, 507286, "SRX26116354", "SRS22679893", "SRA2089519", "Institute of Molecular Genetic and Genetic Engineering", "Institute of Molecular Genetic and Genetic Engineering", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Serbia", "2024-09-18", "Adult", "Adult", "Muscle", "Muscular System"], [33826, "SRR30712582", "SRX26116353", "SRS22679892", "SRP533374", "PRJNA1162497", "Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish", "GSE277480", "Transcriptome Analysis", "The ANKRD1 gene is responsive to different forms of mechanical stress including injury stretching resistance exercise and eccentric contractions. We showed that ankrd1a zebrafish homologue of mammalian ANKRD1 gets activated in the heart post cryoinjury of the ventricle and in skeletal muscle post stab wound suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction muscle cell differentiation MAPK and integrin mediated signaling pathways and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery RNA was isolated from the muscle tissue around the injury anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt non injured wt injured mutant and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.", null, null, null, "wt I 3", "GSM8523052", null, "source name:skeletal muscle|tissue:skeletal muscle|genotype:wt|treatment:injured|geo loc name:missing|collection date:missing", "wt I 3", "fastp v0.23.4 STAR v2.7.0 RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20 nqualified percent limit=30 average qual=25 low complexity filter=True complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110 Ensembl v110 using STAR v2.7.10 with standard parameters except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3 to estimate transcript and gene abundances. Subsequently the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110 Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample", "skeletal muscle", "Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail in line with the anal opening. Immediately post the injury fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle just behind the anal opening and containing the injury area anterior and posterior to the needle lesion was dissected by a razor blade and used for RNA isolation.", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", "Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions in circulating water system under 14 h light/10 h dark cycle and at 28.5 \u25e6C.", "tissue:skeletal muscle|genotype:wt|treatment:injured", "GSM8523052", "GSM8523052: wt I 3; Danio rerio; RNA Seq", "GSM8523052 r1", "GSM8523052", "1", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP533374", null, null, "1525060_S25_R1_001.fastq.gz 1525060_S25_R2_001.fastq.gz", "fastq fastq", 9028185508.0, 29894654.0, "GSM8523052 r1", "0:151 1:151", "A:2276450364;C:2258194222;G:2134851710;T:2358181229;N:507983", 151, 151, null, null, 2276450364, 2258194222, 2134851710, 2358181229, 507983, "SRX26116353", "SRS22679892", "SRA2089519", "Institute of Molecular Genetic and Genetic Engineering", "Institute of Molecular Genetic and Genetic Engineering", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Serbia", "2024-09-18", "Adult", "Adult", "Muscle", "Muscular System"], [33827, "SRR30712583", "SRX26116352", "SRS22679891", "SRP533374", "PRJNA1162497", "Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish", "GSE277480", "Transcriptome Analysis", "The ANKRD1 gene is responsive to different forms of mechanical stress including injury stretching resistance exercise and eccentric contractions. We showed that ankrd1a zebrafish homologue of mammalian ANKRD1 gets activated in the heart post cryoinjury of the ventricle and in skeletal muscle post stab wound suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction muscle cell differentiation MAPK and integrin mediated signaling pathways and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery RNA was isolated from the muscle tissue around the injury anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt non injured wt injured mutant and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.", null, null, null, "wt I 2", "GSM8523051", null, "source name:skeletal muscle|tissue:skeletal muscle|genotype:wt|treatment:injured|geo loc name:missing|collection date:missing", "wt I 2", "fastp v0.23.4 STAR v2.7.0 RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20 nqualified percent limit=30 average qual=25 low complexity filter=True complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110 Ensembl v110 using STAR v2.7.10 with standard parameters except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3 to estimate transcript and gene abundances. Subsequently the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110 Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample", "skeletal muscle", "Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail in line with the anal opening. Immediately post the injury fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle just behind the anal opening and containing the injury area anterior and posterior to the needle lesion was dissected by a razor blade and used for RNA isolation.", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", "Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions in circulating water system under 14 h light/10 h dark cycle and at 28.5 \u25e6C.", "tissue:skeletal muscle|genotype:wt|treatment:injured", "GSM8523051", "GSM8523051: wt I 2; Danio rerio; RNA Seq", "GSM8523051 r1", "GSM8523051", "1", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP533374", null, null, "1525059_S24_R1_001.fastq.gz 1525059_S24_R2_001.fastq.gz", "fastq fastq", 8553382920.0, 28322460.0, "GSM8523051 r1", "0:151 1:151", "A:2189680208;C:2131369869;G:1994221174;T:2237623798;N:487871", 151, 151, null, null, 2189680208, 2131369869, 1994221174, 2237623798, 487871, "SRX26116352", "SRS22679891", "SRA2089519", "Institute of Molecular Genetic and Genetic Engineering", "Institute of Molecular Genetic and Genetic Engineering", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Serbia", "2024-09-18", "Adult", "Adult", "Muscle", "Muscular System"], [33828, "SRR30712584", "SRX26116351", "SRS22679890", "SRP533374", "PRJNA1162497", "Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish", "GSE277480", "Transcriptome Analysis", "The ANKRD1 gene is responsive to different forms of mechanical stress including injury stretching resistance exercise and eccentric contractions. We showed that ankrd1a zebrafish homologue of mammalian ANKRD1 gets activated in the heart post cryoinjury of the ventricle and in skeletal muscle post stab wound suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction muscle cell differentiation MAPK and integrin mediated signaling pathways and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery RNA was isolated from the muscle tissue around the injury anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt non injured wt injured mutant and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.", null, null, null, "wt I 1", "GSM8523050", null, "source name:skeletal muscle|tissue:skeletal muscle|genotype:wt|treatment:injured|geo loc name:missing|collection date:missing", "wt I 1", "fastp v0.23.4 STAR v2.7.0 RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20 nqualified percent limit=30 average qual=25 low complexity filter=True complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110 Ensembl v110 using STAR v2.7.10 with standard parameters except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3 to estimate transcript and gene abundances. Subsequently the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110 Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample", "skeletal muscle", "Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail in line with the anal opening. Immediately post the injury fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle just behind the anal opening and containing the injury area anterior and posterior to the needle lesion was dissected by a razor blade and used for RNA isolation.", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", "Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions in circulating water system under 14 h light/10 h dark cycle and at 28.5 \u25e6C.", "tissue:skeletal muscle|genotype:wt|treatment:injured", "GSM8523050", "GSM8523050: wt I 1; Danio rerio; RNA Seq", "GSM8523050 r1", "GSM8523050", "1", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP533374", null, null, "1525058_S23_R1_001.fastq.gz 1525058_S23_R2_001.fastq.gz", "fastq fastq", 9259618074.0, 30660987.0, "GSM8523050 r1", "0:151 1:151", "A:2353088871;C:2323613307;G:2175738215;T:2406648342;N:529339", 151, 151, null, null, 2353088871, 2323613307, 2175738215, 2406648342, 529339, "SRX26116351", "SRS22679890", "SRA2089519", "Institute of Molecular Genetic and Genetic Engineering", "Institute of Molecular Genetic and Genetic Engineering", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Serbia", "2024-09-18", "Adult", "Adult", "Muscle", "Muscular System"], [33829, "SRR30712585", "SRX26116350", "SRS22679889", "SRP533374", "PRJNA1162497", "Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish", "GSE277480", "Transcriptome Analysis", "The ANKRD1 gene is responsive to different forms of mechanical stress including injury stretching resistance exercise and eccentric contractions. We showed that ankrd1a zebrafish homologue of mammalian ANKRD1 gets activated in the heart post cryoinjury of the ventricle and in skeletal muscle post stab wound suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction muscle cell differentiation MAPK and integrin mediated signaling pathways and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery RNA was isolated from the muscle tissue around the injury anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt non injured wt injured mutant and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.", null, null, null, "wt NI 4", "GSM8523049", null, "source name:skeletal muscle|tissue:skeletal muscle|genotype:wt|treatment:non injured|geo loc name:missing|collection date:missing", "wt NI 4", "fastp v0.23.4 STAR v2.7.0 RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20 nqualified percent limit=30 average qual=25 low complexity filter=True complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110 Ensembl v110 using STAR v2.7.10 with standard parameters except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3 to estimate transcript and gene abundances. Subsequently the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110 Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample", "skeletal muscle", "Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail in line with the anal opening. Immediately post the injury fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle just behind the anal opening and containing the injury area anterior and posterior to the needle lesion was dissected by a razor blade and used for RNA isolation.", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", "Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions in circulating water system under 14 h light/10 h dark cycle and at 28.5 \u25e6C.", "tissue:skeletal muscle|genotype:wt|treatment:non injured", "GSM8523049", "GSM8523049: wt NI 4; Danio rerio; RNA Seq", "GSM8523049 r1", "GSM8523049", "1", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP533374", null, null, "1525057_S22_R1_001.fastq.gz 1525057_S22_R2_001.fastq.gz", "fastq fastq", 8893456966.0, 29448533.0, "GSM8523049 r1", "0:151 1:151", "A:2300319776;C:2180302865;G:2044621569;T:2367713263;N:499493", 151, 151, null, null, 2300319776, 2180302865, 2044621569, 2367713263, 499493, "SRX26116350", "SRS22679889", "SRA2089519", "Institute of Molecular Genetic and Genetic Engineering", "Institute of Molecular Genetic and Genetic Engineering", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Serbia", "2024-09-18", "Adult", "Adult", "Muscle", "Muscular System"], [33830, "SRR30712586", "SRX26116349", "SRS22679888", "SRP533374", "PRJNA1162497", "Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish", "GSE277480", "Transcriptome Analysis", "The ANKRD1 gene is responsive to different forms of mechanical stress including injury stretching resistance exercise and eccentric contractions. We showed that ankrd1a zebrafish homologue of mammalian ANKRD1 gets activated in the heart post cryoinjury of the ventricle and in skeletal muscle post stab wound suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction muscle cell differentiation MAPK and integrin mediated signaling pathways and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery RNA was isolated from the muscle tissue around the injury anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt non injured wt injured mutant and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.", null, null, null, "wt NI 3", "GSM8523048", null, "source name:skeletal muscle|tissue:skeletal muscle|genotype:wt|treatment:non injured|geo loc name:missing|collection date:missing", "wt NI 3", "fastp v0.23.4 STAR v2.7.0 RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20 nqualified percent limit=30 average qual=25 low complexity filter=True complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110 Ensembl v110 using STAR v2.7.10 with standard parameters except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3 to estimate transcript and gene abundances. Subsequently the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110 Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample", "skeletal muscle", "Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail in line with the anal opening. Immediately post the injury fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle just behind the anal opening and containing the injury area anterior and posterior to the needle lesion was dissected by a razor blade and used for RNA isolation.", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", "Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions in circulating water system under 14 h light/10 h dark cycle and at 28.5 \u25e6C.", "tissue:skeletal muscle|genotype:wt|treatment:non injured", "GSM8523048", "GSM8523048: wt NI 3; Danio rerio; RNA Seq", "GSM8523048 r1", "GSM8523048", "1", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP533374", null, null, "1525056_S21_R1_001.fastq.gz 1525056_S21_R2_001.fastq.gz", "fastq fastq", 9463183590.0, 31335045.0, "GSM8523048 r1", "0:151 1:151", "A:2390372740;C:2375512221;G:2247572478;T:2449199968;N:526183", 151, 151, null, null, 2390372740, 2375512221, 2247572478, 2449199968, 526183, "SRX26116349", "SRS22679888", "SRA2089519", "Institute of Molecular Genetic and Genetic Engineering", "Institute of Molecular Genetic and Genetic Engineering", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Serbia", "2024-09-18", "Adult", "Adult", "Muscle", "Muscular System"], [33831, "SRR30712587", "SRX26116348", "SRS22679887", "SRP533374", "PRJNA1162497", "Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish", "GSE277480", "Transcriptome Analysis", "The ANKRD1 gene is responsive to different forms of mechanical stress including injury stretching resistance exercise and eccentric contractions. We showed that ankrd1a zebrafish homologue of mammalian ANKRD1 gets activated in the heart post cryoinjury of the ventricle and in skeletal muscle post stab wound suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction muscle cell differentiation MAPK and integrin mediated signaling pathways and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery RNA was isolated from the muscle tissue around the injury anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt non injured wt injured mutant and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.", null, null, null, "wt NI 2", "GSM8523047", null, "source name:skeletal muscle|tissue:skeletal muscle|genotype:wt|treatment:non injured|geo loc name:missing|collection date:missing", "wt NI 2", "fastp v0.23.4 STAR v2.7.0 RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20 nqualified percent limit=30 average qual=25 low complexity filter=True complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110 Ensembl v110 using STAR v2.7.10 with standard parameters except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3 to estimate transcript and gene abundances. Subsequently the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110 Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample", "skeletal muscle", "Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail in line with the anal opening. Immediately post the injury fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle just behind the anal opening and containing the injury area anterior and posterior to the needle lesion was dissected by a razor blade and used for RNA isolation.", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", "Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions in circulating water system under 14 h light/10 h dark cycle and at 28.5 \u25e6C.", "tissue:skeletal muscle|genotype:wt|treatment:non injured", "GSM8523047", "GSM8523047: wt NI 2; Danio rerio; RNA Seq", "GSM8523047 r1", "GSM8523047", "1", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP533374", null, null, "1525055_S20_R1_001.fastq.gz 1525055_S20_R2_001.fastq.gz", "fastq fastq", 9106987274.0, 30155587.0, "GSM8523047 r1", "0:151 1:151", "A:2302703752;C:2289138612;G:2158041789;T:2356585481;N:517640", 151, 151, null, null, 2302703752, 2289138612, 2158041789, 2356585481, 517640, "SRX26116348", "SRS22679887", "SRA2089519", "Institute of Molecular Genetic and Genetic Engineering", "Institute of Molecular Genetic and Genetic Engineering", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Serbia", "2024-09-18", "Adult", "Adult", "Muscle", "Muscular System"], [33832, "SRR30712588", "SRX26116347", "SRS22679886", "SRP533374", "PRJNA1162497", "Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish", "GSE277480", "Transcriptome Analysis", "The ANKRD1 gene is responsive to different forms of mechanical stress including injury stretching resistance exercise and eccentric contractions. We showed that ankrd1a zebrafish homologue of mammalian ANKRD1 gets activated in the heart post cryoinjury of the ventricle and in skeletal muscle post stab wound suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 xxx post injury. Non injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction muscle cell differentiation MAPK and integrin mediated signaling pathways and cell substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish. Overall design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. post 5 days of recovery RNA was isolated from the muscle tissue around the injury anterior and posterior to the needle lesion or corresponding non injured region in control fish. Four experimental groups injured wt non injured wt injured mutant and non injured mutant were subjected to RNA seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.", null, null, null, "wt NI 1", "GSM8523046", null, "source name:skeletal muscle|tissue:skeletal muscle|genotype:wt|treatment:non injured|geo loc name:missing|collection date:missing", "wt NI 1", "fastp v0.23.4 STAR v2.7.0 RSEM v1.3.3 Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 qualified quality phred=20 nqualified percent limit=30 average qual=25 low complexity filter=True complexity threshold=30 passing filter reads were mapped to the genome reference Danio rerio GRCz11v110 Ensembl v110 using STAR v2.7.10 with standard parameters except for the sjdbOverhang option set on read length Genome and transcripts annotation provided as input were downloaded from Ensembl v110 repository. Alignments were then elaborated by RSEM v1.3.3 to estimate transcript and gene abundances. Subsequently the sample specific gene level abundances were merged into a single raw expression matrix applying a dedicated RSEM command rsem generate data matrix. Assembly: Danio rerio GRCz11v110 Ensembl v110 Supplementary files format and content: tab deliminated text file includes raw counts for each sample", "skeletal muscle", "Muscle injury was performed on tricaine anaesthetised adult zebrafish by inserting and withdrawing a needle into the dorsal myotome of the tail in line with the anal opening. Immediately post the injury fish were transferred to system water for recovery and maintained under standard conditions for 5 days until analysis. The part of the caudal peduncle just behind the anal opening and containing the injury area anterior and posterior to the needle lesion was dissected by a razor blade and used for RNA isolation.", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", "Wild type wt fish AB Oregon and ankrd1abns502 mut were maintained under standard conditions in circulating water system under 14 h light/10 h dark cycle and at 28.5 \u25e6C.", "tissue:skeletal muscle|genotype:wt|treatment:non injured", "GSM8523046", "GSM8523046: wt NI 1; Danio rerio; RNA Seq", "GSM8523046 r1", "GSM8523046", "1", "Skeletal muscle tissue dissected out from the region around the injury and complementary region of non injured wt and ankrd1a / fish was homogenized in TRIzol Reagen Invitorgen Thermo Fisher Scientific USA and total RNA was extracted using RNA Clean and concentrator kit ZYMO Research USA according to the manufacturer instructions. Total RNA was eluted in 25 \u00b5l of RNase free water and its quantity and purity were measured promptly post isolation using BioSpec nano Shimadzu Japan and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM Thermo Scientific Fisher USA. cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit Illumina California USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP533374", null, null, "1525054_S19_R1_001.fastq.gz 1525054_S19_R2_001.fastq.gz", "fastq fastq", 6862974160.0, 22725080.0, "GSM8523046 r1", "0:151 1:151", "A:1767442745;C:1673075382;G:1598164146;T:1823910942;N:380945", 151, 151, null, null, 1767442745, 1673075382, 1598164146, 1823910942, 380945, "SRX26116347", "SRS22679886", "SRA2089519", "Institute of Molecular Genetic and Genetic Engineering", "Institute of Molecular Genetic and Genetic Engineering", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Serbia", "2024-09-18", "Adult", "Adult", "Muscle", "Muscular System"], [37105, "SRR891510", "SRX298190", "SRS673880", "SRP024369", "PRJNA207719", "Tissue specific transcriptome profiling of zebrafish", "PRJNA207719", "Other", "Tissue specific transcriptome profiling of zebrafish.", null, null, null, null, "Danio rerio muscle", null, "sex:missing|strain:wild type|tissue:muscle|health state:normal|collection date:2013|geo loc name:India|biomaterial provider:CSIR Institute of Genomics and Integrative Biology|age:adult|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Tissue specific transcriptome of zebrafish", "Transcriptome of zebrafish Danio rerio muscle", "zebrafish muscle", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", "1020Application ReadForward11Application ReadReverse52", "SRP024369", null, null, "lane4_NoIndex_L004_R1_cat.fastq lane4_NoIndex_L004_R2_cat.fastq", "fastq fastq", 1895673468.0, 18585034.0, "Transcriptome of zebrafish Danio rerio muscle", "0:51 1:51", "A:461627994;C:495899684;G:489490468;T:448396921;N:258401", 51, 51, null, null, 461627994, 495899684, 489490468, 448396921, 258401, "SRX298190", "SRS673880", "SRA089174", "CSIR-IGIB", "CSIR-Institute of Genomics and Integrative Biology CSIR-Institute of Genomics and Integrative Biology", 2, 0.90619, 0.93507, 0.0338, 0.03473, 0.79267, 0.78683, 0.45256, 0.45438, 51, 51, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2013-10-10", "Adult", "Adult", "Muscle", "Muscular System"], [38063, "SRR1524241", "SRX661006", "SRS665981", "SRP044781", "PRJNA255848", "Danio rerio Transcriptome", "PRJNA255848", "Transcriptome Analysis", "Transcriptome analysis of 12 zebrafish tissues", "parent bioproject:PRJNA255979", "pubmed:27189481", "Zebrafish Muscle", "Zebrafish Muscle", "F Dr 5", null, "strain:AB|age:5 month|biomaterial provider:INRA|sex:female|tissue:Muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish Muscle", "F Dr 5", "F Dr 5", "Total RNA was qualified using an Agilent BioAnalyzer and 1 \u00b5g was used for polyA selection and library construction with Illumina's TruSeq stranded total RNA sample preparation kit according to the manufacturer's instructions TruSeq stranded total RNA SamplePrep Guide RevC", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "SRP044781", null, null, "F_Dr_5_CGATGT_L002_R1.fastq.gz F_Dr_5_CGATGT_L002_R2.fastq.gz", "fastq fastq", 6806595200.0, 34032976.0, "F Dr 5 files", "0:100 1:100", "A:1732271631;C:1678982446;G:1678662020;T:1710896201;N:5782902", 100, 100, null, null, 1732271631, 1678982446, 1678662020, 1710896201, 5782902, "SRX661006", "SRS665981", "SRA176464", "INRA|Fish Physiology and Genomics", "INRA PhyloFish", 2, 0.9665, 0.96619, 0.03055, 0.03064, 0.78336, 0.78366, 0.51756, 0.51698, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "France", "2015-07-24", "Adult", "Adult", "Muscle", "Muscular System"], [38260, "SRR1609755", "SRX730408", "SRS719629", "SRP048807", "PRJNA263496", "Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish", "GSE62221", "Transcriptome Analysis", "The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28\u00b0C to mild 18\u00b0C and severe 10\u00b0C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as \u2018negative regulation of endopeptidase activity\u2019 in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures", null, "pubmed:26227973", null, "muscle10", "GSM1523050", null, "source name:muscle|tissue:muscle|temperature:10\u00b0C|strain:Tubingen|age:6 mpf", "muscle10", "Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "muscle", "fish were maintained 12h to adapt low temperatures and then killed by pithing", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:muscle|temperature:10\u00b0C|strain:Tubingen|age:6 mpf", "GSM1523050", "GSM1523050: muscle10; Danio rerio; RNA Seq", "GSM1523050", null, "1", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1523050", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP048807", null, null, "muscle10_1.fq.gz muscle10_2.fq.gz", "fastq fastq", 3526303600.0, 17631518.0, "GSM1523050 r1", "0:100 1:100", "A:907821899;C:862068806;G:861677127;T:894668376;N:67392", 100, 100, null, null, 907821899, 862068806, 861677127, 894668376, 67392, "SRX730408", "SRS719629", "SRA189240", "GEO", "Shanghai Ocean University", 2, 0.97117, 0.96598, 0.02645, 0.02677, 0.78376, 0.78819, 0.49847, 0.49607, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-10-09", "Adult", "Adult", "Muscle", "Muscular System"], [38261, "SRR1609754", "SRX730407", "SRS719627", "SRP048807", "PRJNA263496", "Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish", "GSE62221", "Transcriptome Analysis", "The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28\u00b0C to mild 18\u00b0C and severe 10\u00b0C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as \u2018negative regulation of endopeptidase activity\u2019 in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures", null, "pubmed:26227973", null, "muscle18", "GSM1523049", null, "source name:muscle|tissue:muscle|temperature:18\u00b0C|strain:Tubingen|age:6 mpf", "muscle18", "Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "muscle", "fish were maintained 12h to adapt low temperatures and then killed by pithing", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:muscle|temperature:18\u00b0C|strain:Tubingen|age:6 mpf", "GSM1523049", "GSM1523049: muscle18; Danio rerio; RNA Seq", "GSM1523049", null, "1", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1523049", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP048807", null, null, "muscle18_2.fq.gz muscle18_1.fq.gz", "fastq fastq", 3052105000.0, 15260525.0, "GSM1523049 r1", "0:100 1:100", "A:792718670;C:735445281;G:733127780;T:781512064;N:9301205", 100, 100, null, null, 792718670, 735445281, 733127780, 781512064, 9301205, "SRX730407", "SRS719627", "SRA189240", "GEO", "Shanghai Ocean University", 2, 0.95747, 0.94738, 0.02778, 0.0283, 0.83313, 0.84064, 0.50113, 0.48506, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-10-09", "Adult", "Adult", "Muscle", "Muscular System"], [38262, "SRR1609753", "SRX730406", "SRS719626", "SRP048807", "PRJNA263496", "Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish", "GSE62221", "Transcriptome Analysis", "The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28\u00b0C to mild 18\u00b0C and severe 10\u00b0C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as \u2018negative regulation of endopeptidase activity\u2019 in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures", null, "pubmed:26227973", null, "muscle28", "GSM1523048", null, "source name:muscle|tissue:muscle|temperature:28\u00b0C|strain:Tubingen|age:6 mpf", "muscle28", "Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "muscle", "fish were maintained 12h to adapt low temperatures and then killed by pithing", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:muscle|temperature:28\u00b0C|strain:Tubingen|age:6 mpf", "GSM1523048", "GSM1523048: muscle28; Danio rerio; RNA Seq", "GSM1523048", null, "1", "Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1523048", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP048807", null, null, "muscle28_2.fq.gz muscle28_1.fq.gz", "fastq fastq", 3631962400.0, 18159812.0, "GSM1523048 r1", "0:100 1:100", "A:939417649;C:881759212;G:878258318;T:932460271;N:66950", 100, 100, null, null, 939417649, 881759212, 878258318, 932460271, 66950, "SRX730406", "SRS719626", "SRA189240", "GEO", "Shanghai Ocean University", 2, 0.96957, 0.96709, 0.02715, 0.02728, 0.80748, 0.80947, 0.52321, 0.52681, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-10-09", "Adult", "Adult", "Muscle", "Muscular System"], [40779, "SRR3381875", "SRX1704286", "SRS1396337", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 3 muscle", "GSM2122877", null, "source name:muscle cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "Treated 3 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "GSM2122877", "GSM2122877: Treated 3 muscle; Danio rerio; RNA Seq", "GSM2122877", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122877", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s6_2_GSLv3-7_44_SL139801.fastq.gz C8DY1ANXX_s6_1_GSLv3-7_44_SL139801.fastq.gz", "fastq fastq", 1424344100.0, 14243441.0, "GSM2122877 r1", "0:50 1:50", "A:373105926;C:339772973;G:338044082;T:373286793;N:134326", 50, 50, null, null, 373105926, 339772973, 338044082, 373286793, 134326, "SRX1704286", "SRS1396337", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95482, 0.95657, 0.03881, 0.03832, 0.73038, 0.73046, 0.518, 0.51502, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40780, "SRR3381876", "SRX1704286", "SRS1396337", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 3 muscle", "GSM2122877", null, "source name:muscle cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "Treated 3 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "GSM2122877", "GSM2122877: Treated 3 muscle; Danio rerio; RNA Seq", "GSM2122877", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122877", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s6_1_GSLv3-7_44_SL139801.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_44_SL139801.fastq.gz", "fastq fastq", 1067179600.0, 10671796.0, "GSM2122877 r2", "0:50 1:50", "A:277281148;C:254793697;G:251033742;T:284052011;N:19002", 50, 50, null, null, 277281148, 254793697, 251033742, 284052011, 19002, "SRX1704286", "SRS1396337", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95567, 0.95769, 0.03847, 0.03979, 0.74862, 0.73651, 0.52799, 0.52237, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40781, "SRR3381877", "SRX1704286", "SRS1396337", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 3 muscle", "GSM2122877", null, "source name:muscle cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "Treated 3 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "GSM2122877", "GSM2122877: Treated 3 muscle; Danio rerio; RNA Seq", "GSM2122877", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122877", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s5_1_GSLv3-7_44_SL139801.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_44_SL139801.fastq.gz", "fastq fastq", 1419623200.0, 14196232.0, "GSM2122877 r3", "0:50 1:50", "A:371804107;C:338707464;G:337012958;T:371929117;N:169554", 50, 50, null, null, 371804107, 338707464, 337012958, 371929117, 169554, "SRX1704286", "SRS1396337", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95359, 0.95717, 0.0391, 0.03926, 0.73219, 0.73225, 0.5178, 0.51875, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40782, "SRR3381878", "SRX1704286", "SRS1396337", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 3 muscle", "GSM2122877", null, "source name:muscle cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "Treated 3 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "GSM2122877", "GSM2122877: Treated 3 muscle; Danio rerio; RNA Seq", "GSM2122877", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122877", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s5_1_GSLv3-7_44_SL139801.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_44_SL139801.fastq.gz", "fastq fastq", 1080171600.0, 10801716.0, "GSM2122877 r4", "0:50 1:50", "A:280638393;C:258100474;G:254205905;T:287207620;N:19208", 50, 50, null, null, 280638393, 258100474, 254205905, 287207620, 19208, "SRX1704286", "SRS1396337", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95677, 0.95714, 0.03833, 0.03933, 0.74994, 0.73937, 0.52539, 0.52283, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40783, "SRR3381871", "SRX1704285", "SRS1396338", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 2 muscle", "GSM2122876", null, "source name:muscle cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "Treated 2 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "GSM2122876", "GSM2122876: Treated 2 muscle; Danio rerio; RNA Seq", "GSM2122876", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122876", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s5_1_GSLv3-7_43_SL139800.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_43_SL139800.fastq.gz", "fastq fastq", 1066008900.0, 10660089.0, "GSM2122876 r1", "0:50 1:50", "A:275324871;C:257800561;G:252695833;T:280167714;N:19921", 50, 50, null, null, 275324871, 257800561, 252695833, 280167714, 19921, "SRX1704285", "SRS1396338", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.96433, 0.96552, 0.05349, 0.05444, 0.78151, 0.77007, 0.56137, 0.54847, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40784, "SRR3381872", "SRX1704285", "SRS1396338", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 2 muscle", "GSM2122876", null, "source name:muscle cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "Treated 2 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "GSM2122876", "GSM2122876: Treated 2 muscle; Danio rerio; RNA Seq", "GSM2122876", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122876", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s6_1_GSLv3-7_43_SL139800.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_43_SL139800.fastq.gz", "fastq fastq", 1389737800.0, 13897378.0, "GSM2122876 r2", "0:50 1:50", "A:362133250;C:335227403;G:331835484;T:360399948;N:141715", 50, 50, null, null, 362133250, 335227403, 331835484, 360399948, 141715, "SRX1704285", "SRS1396338", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.96312, 0.96504, 0.05473, 0.05481, 0.76096, 0.76327, 0.54262, 0.53783, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40785, "SRR3381873", "SRX1704285", "SRS1396338", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 2 muscle", "GSM2122876", null, "source name:muscle cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "Treated 2 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "GSM2122876", "GSM2122876: Treated 2 muscle; Danio rerio; RNA Seq", "GSM2122876", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122876", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s6_1_GSLv3-7_43_SL139800.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_43_SL139800.fastq.gz", "fastq fastq", 1049220700.0, 10492207.0, "GSM2122876 r3", "0:50 1:50", "A:271022900;C:253544145;G:248558843;T:276075122;N:19690", 50, 50, null, null, 271022900, 253544145, 248558843, 276075122, 19690, "SRX1704285", "SRS1396338", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.96446, 0.96516, 0.05382, 0.05449, 0.78269, 0.77072, 0.55933, 0.54576, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40786, "SRR3381874", "SRX1704285", "SRS1396338", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 2 muscle", "GSM2122876", null, "source name:muscle cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "Treated 2 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "GSM2122876", "GSM2122876: Treated 2 muscle; Danio rerio; RNA Seq", "GSM2122876", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122876", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s5_1_GSLv3-7_43_SL139800.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_43_SL139800.fastq.gz", "fastq fastq", 1394669100.0, 13946691.0, "GSM2122876 r4", "0:50 1:50", "A:363332129;C:336439374;G:333102129;T:361606902;N:188566", 50, 50, null, null, 363332129, 336439374, 333102129, 361606902, 188566, "SRX1704285", "SRS1396338", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.96262, 0.96516, 0.05541, 0.05531, 0.76262, 0.76516, 0.54009, 0.54486, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40787, "SRR3381865", "SRX1704284", "SRS1396339", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 1 muscle", "GSM2122875", null, "source name:muscle cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "Treated 1 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "GSM2122875", "GSM2122875: Treated 1 muscle; Danio rerio; RNA Seq", "GSM2122875", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122875", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s6_1_GSLv3-7_42_SL139799.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_42_SL139799.fastq.gz", "fastq fastq", 848332400.0, 8483324.0, "GSM2122875 r1", "0:50 1:50", "A:222562905;C:202678911;G:201260703;T:221751638;N:78243", 50, 50, null, null, 222562905, 202678911, 201260703, 221751638, 78243, "SRX1704284", "SRS1396339", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95805, 0.961, 0.04973, 0.0491, 0.74509, 0.74446, 0.53696, 0.53656, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40788, "SRR3381866", "SRX1704284", "SRS1396339", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 1 muscle", "GSM2122875", null, "source name:muscle cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "Treated 1 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "GSM2122875", "GSM2122875: Treated 1 muscle; Danio rerio; RNA Seq", "GSM2122875", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122875", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s5_1_GSLv3-7_42_SL139799.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_42_SL139799.fastq.gz", "fastq fastq", 847234900.0, 8472349.0, "GSM2122875 r2", "0:50 1:50", "A:222218092;C:202466432;G:201066152;T:221372059;N:112165", 50, 50, null, null, 222218092, 202466432, 201066152, 221372059, 112165, "SRX1704284", "SRS1396339", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95894, 0.96214, 0.04899, 0.04888, 0.74332, 0.74353, 0.53693, 0.53748, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40789, "SRR3381867", "SRX1704284", "SRS1396339", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 1 muscle", "GSM2122875", null, "source name:muscle cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "Treated 1 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "GSM2122875", "GSM2122875: Treated 1 muscle; Danio rerio; RNA Seq", "GSM2122875", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122875", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DKGANXX_s8_2_GSLv3-7_42_SL139799.fastq.gz C8DKGANXX_s8_1_GSLv3-7_42_SL139799.fastq.gz", "fastq fastq", 1573927200.0, 15739272.0, "GSM2122875 r3", "0:50 1:50", "A:413612028;C:375148773;G:371885800;T:412450020;N:830579", 50, 50, null, null, 413612028, 375148773, 371885800, 412450020, 830579, "SRX1704284", "SRS1396339", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95668, 0.96042, 0.05044, 0.04996, 0.74588, 0.74763, 0.54005, 0.5409, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40790, "SRR3381868", "SRX1704284", "SRS1396339", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 1 muscle", "GSM2122875", null, "source name:muscle cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "Treated 1 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "GSM2122875", "GSM2122875: Treated 1 muscle; Danio rerio; RNA Seq", "GSM2122875", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122875", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s5_1_GSLv3-7_42_SL139799.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_42_SL139799.fastq.gz", "fastq fastq", 646111500.0, 6461115.0, "GSM2122875 r4", "0:50 1:50", "A:168189077;C:154670722;G:152078186;T:171161973;N:11542", 50, 50, null, null, 168189077, 154670722, 152078186, 171161973, 11542, "SRX1704284", "SRS1396339", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.96133, 0.96206, 0.04804, 0.04976, 0.76568, 0.75126, 0.5261, 0.54393, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40791, "SRR3381869", "SRX1704284", "SRS1396339", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 1 muscle", "GSM2122875", null, "source name:muscle cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "Treated 1 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "GSM2122875", "GSM2122875: Treated 1 muscle; Danio rerio; RNA Seq", "GSM2122875", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122875", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DKGANXX_s7_1_GSLv3-7_42_SL139799.fastq.gz C8DKGANXX_s7_2_GSLv3-7_42_SL139799.fastq.gz", "fastq fastq", 1577881700.0, 15778817.0, "GSM2122875 r5", "0:50 1:50", "A:414672587;C:376155159;G:372910894;T:413443352;N:699708", 50, 50, null, null, 414672587, 376155159, 372910894, 413443352, 699708, "SRX1704284", "SRS1396339", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95735, 0.96122, 0.05005, 0.0498, 0.74789, 0.7486, 0.53779, 0.52556, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40792, "SRR3381870", "SRX1704284", "SRS1396339", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Treated 1 muscle", "GSM2122875", null, "source name:muscle cortisol|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "Treated 1 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle cortisol", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:cortisol", "GSM2122875", "GSM2122875: Treated 1 muscle; Danio rerio; RNA Seq", "GSM2122875", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122875", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s6_2_GSLv3-7_42_SL139799.fastq.gz C8BH2ANXX_s6_1_GSLv3-7_42_SL139799.fastq.gz", "fastq fastq", 637889100.0, 6378891.0, "GSM2122875 r6", "0:50 1:50", "A:166073650;C:152564175;G:150056875;T:169183109;N:11291", 50, 50, null, null, 166073650, 152564175, 150056875, 169183109, 11291, "SRX1704284", "SRS1396339", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95944, 0.96139, 0.04768, 0.04952, 0.7651, 0.75126, 0.544, 0.52652, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40793, "SRR3381859", "SRX1704283", "SRS1396340", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 3 muscle", "GSM2122874", null, "source name:muscle DMSO control|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "Control 3 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "GSM2122874", "GSM2122874: Control 3 muscle; Danio rerio; RNA Seq", "GSM2122874", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122874", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s5_1_GSLv3-7_41_SL139798.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_41_SL139798.fastq.gz", "fastq fastq", 787547200.0, 7875472.0, "GSM2122874 r1", "0:50 1:50", "A:203942710;C:188877712;G:185633192;T:209079402;N:14184", 50, 50, null, null, 203942710, 188877712, 185633192, 209079402, 14184, "SRX1704283", "SRS1396340", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95198, 0.95438, 0.04503, 0.04557, 0.75012, 0.73823, 0.51181, 0.50673, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40794, "SRR3381860", "SRX1704283", "SRS1396340", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 3 muscle", "GSM2122874", null, "source name:muscle DMSO control|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "Control 3 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "GSM2122874", "GSM2122874: Control 3 muscle; Danio rerio; RNA Seq", "GSM2122874", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122874", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s6_1_GSLv3-7_41_SL139798.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_41_SL139798.fastq.gz", "fastq fastq", 777871300.0, 7778713.0, "GSM2122874 r2", "0:50 1:50", "A:201401204;C:186411928;G:183267013;T:206776804;N:14351", 50, 50, null, null, 201401204, 186411928, 183267013, 206776804, 14351, "SRX1704283", "SRS1396340", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95178, 0.95334, 0.04567, 0.04614, 0.75, 0.73809, 0.50747, 0.50517, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40795, "SRR3381861", "SRX1704283", "SRS1396340", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 3 muscle", "GSM2122874", null, "source name:muscle DMSO control|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "Control 3 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "GSM2122874", "GSM2122874: Control 3 muscle; Danio rerio; RNA Seq", "GSM2122874", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122874", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s6_1_GSLv3-7_41_SL139798.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_41_SL139798.fastq.gz", "fastq fastq", 1033412900.0, 10334129.0, "GSM2122874 r3", "0:50 1:50", "A:269924492;C:247210780;G:245428656;T:270748401;N:100571", 50, 50, null, null, 269924492, 247210780, 245428656, 270748401, 100571, "SRX1704283", "SRS1396340", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95005, 0.95406, 0.04614, 0.04528, 0.73233, 0.73273, 0.5102, 0.49779, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40796, "SRR3381862", "SRX1704283", "SRS1396340", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 3 muscle", "GSM2122874", null, "source name:muscle DMSO control|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "Control 3 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "GSM2122874", "GSM2122874: Control 3 muscle; Danio rerio; RNA Seq", "GSM2122874", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122874", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DKGANXX_s7_1_GSLv3-7_41_SL139798.fastq.gz C8DKGANXX_s7_2_GSLv3-7_41_SL139798.fastq.gz", "fastq fastq", 1748322200.0, 17483222.0, "GSM2122874 r4", "0:50 1:50", "A:457419358;C:417342674;G:413661922;T:459125785;N:772461", 50, 50, null, null, 457419358, 417342674, 413661922, 459125785, 772461, "SRX1704283", "SRS1396340", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.94986, 0.95275, 0.0456, 0.04501, 0.73519, 0.7361, 0.49935, 0.498, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40797, "SRR3381863", "SRX1704283", "SRS1396340", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 3 muscle", "GSM2122874", null, "source name:muscle DMSO control|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "Control 3 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "GSM2122874", "GSM2122874: Control 3 muscle; Danio rerio; RNA Seq", "GSM2122874", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122874", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DKGANXX_s8_1_GSLv3-7_41_SL139798.fastq.gz C8DKGANXX_s8_2_GSLv3-7_41_SL139798.fastq.gz", "fastq fastq", 1742671200.0, 17426712.0, "GSM2122874 r5", "0:50 1:50", "A:455910914;C:415954064;G:412227260;T:457669615;N:909347", 50, 50, null, null, 455910914, 415954064, 412227260, 457669615, 909347, "SRX1704283", "SRS1396340", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.94773, 0.95304, 0.04728, 0.04677, 0.73533, 0.73626, 0.50896, 0.50825, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40798, "SRR3381864", "SRX1704283", "SRS1396340", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 3 muscle", "GSM2122874", null, "source name:muscle DMSO control|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "Control 3 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "GSM2122874", "GSM2122874: Control 3 muscle; Danio rerio; RNA Seq", "GSM2122874", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122874", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s5_1_GSLv3-7_41_SL139798.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_41_SL139798.fastq.gz", "fastq fastq", 1030442700.0, 10304427.0, "GSM2122874 r6", "0:50 1:50", "A:269126215;C:246494168;G:244810222;T:269890237;N:121858", 50, 50, null, null, 269126215, 246494168, 244810222, 269890237, 121858, "SRX1704283", "SRS1396340", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95052, 0.95489, 0.04548, 0.04564, 0.7318, 0.73223, 0.50139, 0.4967, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40799, "SRR3381855", "SRX1704282", "SRS1396341", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 2 muscle", "GSM2122873", null, "source name:muscle DMSO control|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "Control 2 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "GSM2122873", "GSM2122873: Control 2 muscle; Danio rerio; RNA Seq", "GSM2122873", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122873", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s6_1_GSLv3-7_40_SL139797.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_40_SL139797.fastq.gz", "fastq fastq", 1340415000.0, 13404150.0, "GSM2122873 r1", "0:50 1:50", "A:353946071;C:317969610;G:315652698;T:352704682;N:141939", 50, 50, null, null, 353946071, 317969610, 315652698, 352704682, 141939, "SRX1704282", "SRS1396341", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95374, 0.95721, 0.05644, 0.05543, 0.73148, 0.73093, 0.52277, 0.52413, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40800, "SRR3381856", "SRX1704282", "SRS1396341", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 2 muscle", "GSM2122873", null, "source name:muscle DMSO control|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "Control 2 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "GSM2122873", "GSM2122873: Control 2 muscle; Danio rerio; RNA Seq", "GSM2122873", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122873", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s5_1_GSLv3-7_40_SL139797.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_40_SL139797.fastq.gz", "fastq fastq", 1018469600.0, 10184696.0, "GSM2122873 r2", "0:50 1:50", "A:266827081;C:241977417;G:237977207;T:271668815;N:19080", 50, 50, null, null, 266827081, 241977417, 237977207, 271668815, 19080, "SRX1704282", "SRS1396341", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95433, 0.95645, 0.05437, 0.05552, 0.75055, 0.73549, 0.52431, 0.53091, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40801, "SRR3381857", "SRX1704282", "SRS1396341", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 2 muscle", "GSM2122873", null, "source name:muscle DMSO control|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "Control 2 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "GSM2122873", "GSM2122873: Control 2 muscle; Danio rerio; RNA Seq", "GSM2122873", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122873", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s6_1_GSLv3-7_40_SL139797.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_40_SL139797.fastq.gz", "fastq fastq", 1006378600.0, 10063786.0, "GSM2122873 r3", "0:50 1:50", "A:263706972;C:238906506;G:235012423;T:268734236;N:18463", 50, 50, null, null, 263706972, 238906506, 235012423, 268734236, 18463, "SRX1704282", "SRS1396341", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.9548, 0.95722, 0.05456, 0.05539, 0.75329, 0.73726, 0.53559, 0.52949, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40802, "SRR3381858", "SRX1704282", "SRS1396341", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 2 muscle", "GSM2122873", null, "source name:muscle DMSO control|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "Control 2 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "GSM2122873", "GSM2122873: Control 2 muscle; Danio rerio; RNA Seq", "GSM2122873", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122873", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s5_1_GSLv3-7_40_SL139797.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_40_SL139797.fastq.gz", "fastq fastq", 1336008700.0, 13360087.0, "GSM2122873 r4", "0:50 1:50", "A:352686700;C:317029991;G:314711166;T:351410321;N:170522", 50, 50, null, null, 352686700, 317029991, 314711166, 351410321, 170522, "SRX1704282", "SRS1396341", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95337, 0.95707, 0.05608, 0.05554, 0.73168, 0.73079, 0.52275, 0.51529, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40803, "SRR3381851", "SRX1704281", "SRS1396342", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 1 muscle", "GSM2122872", null, "source name:muscle DMSO control|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "Control 1 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "GSM2122872", "GSM2122872: Control 1 muscle; Danio rerio; RNA Seq", "GSM2122872", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122872", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s5_1_GSLv3-7_39_SL139796.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_39_SL139796.fastq.gz", "fastq fastq", 942420100.0, 9424201.0, "GSM2122872 r1", "0:50 1:50", "A:245877374;C:225467662;G:220622878;T:250434429;N:17757", 50, 50, null, null, 245877374, 225467662, 220622878, 250434429, 17757, "SRX1704281", "SRS1396342", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95903, 0.96153, 0.07221, 0.07346, 0.7866, 0.77354, 0.5369, 0.55657, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40804, "SRR3381852", "SRX1704281", "SRS1396342", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 1 muscle", "GSM2122872", null, "source name:muscle DMSO control|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "Control 1 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "GSM2122872", "GSM2122872: Control 1 muscle; Danio rerio; RNA Seq", "GSM2122872", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122872", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s6_1_GSLv3-7_39_SL139796.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_39_SL139796.fastq.gz", "fastq fastq", 1219958700.0, 12199587.0, "GSM2122872 r2", "0:50 1:50", "A:321337830;C:291082130;G:287532487;T:319888094;N:118159", 50, 50, null, null, 321337830, 291082130, 287532487, 319888094, 118159, "SRX1704281", "SRS1396342", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95782, 0.96009, 0.07535, 0.07403, 0.7666, 0.7679, 0.55312, 0.55091, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40805, "SRR3381853", "SRX1704281", "SRS1396342", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 1 muscle", "GSM2122872", null, "source name:muscle DMSO control|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "Control 1 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "GSM2122872", "GSM2122872: Control 1 muscle; Danio rerio; RNA Seq", "GSM2122872", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122872", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8BH2ANXX_s6_1_GSLv3-7_39_SL139796.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_39_SL139796.fastq.gz", "fastq fastq", 928437800.0, 9284378.0, "GSM2122872 r3", "0:50 1:50", "A:242268974;C:221922831;G:217174138;T:247054793;N:17064", 50, 50, null, null, 242268974, 221922831, 217174138, 247054793, 17064, "SRX1704281", "SRS1396342", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95912, 0.96021, 0.07206, 0.07357, 0.78796, 0.77518, 0.55394, 0.55959, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [40806, "SRR3381854", "SRX1704281", "SRS1396342", "SRP073272", "PRJNA318414", "Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults]", "GSE80260", "Transcriptome Analysis", "Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.", "parent bioproject:PRJNA318502", "pubmed:27444789", null, "Control 1 muscle", "GSM2122872", null, "source name:muscle DMSO control|strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "Control 1 muscle", "Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.", "muscle DMSO control", "DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions.", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.", "strain/background:AB|tissue:muscle|age:adult|embryonic treatment:DMSO", "GSM2122872", "GSM2122872: Control 1 muscle; Danio rerio; RNA Seq", "GSM2122872", null, "1", "RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.", "GEO Accession:GSM2122872", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP073272", null, null, "C8DY1ANXX_s5_1_GSLv3-7_39_SL139796.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_39_SL139796.fastq.gz", "fastq fastq", 1221933900.0, 12219339.0, "GSM2122872 r4", "0:50 1:50", "A:321810541;C:291585356;G:288045217;T:320331102;N:161684", 50, 50, null, null, 321810541, 291585356, 288045217, 320331102, 161684, "SRX1704281", "SRS1396342", "SRA411416", "GEO", "Molecular and Biomedical Sciences, University of Maine", 2, 0.95785, 0.96069, 0.0757, 0.07483, 0.76489, 0.76861, 0.55409, 0.55366, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-13", "Adult", "Adult", "Muscle", "Muscular System"], [41253, "SRR4017375", "SRX2011209", "SRS1608493", "SRP081209", "PRJNA338400", "Systematic identification and characterization of long non coding RNAs in zebrafish through RNA Seq", "GSE85416", "Transcriptome Analysis", "We sequenced mRNA from embryonic heart of zebrafish larvae 4 dpf adult heart of 6 mpf WIK fish and adult muscle of adult fish consisting of both fast twitch and slow twitch fibers. Overall design: Examination of mRNA and long noncoding RNA levels in embryonic heart adult heart and adult muscle tissues", null, "pubmed:28455512", null, "adult muscle 2", "GSM2266462", null, "source name:zebrafish adult muscle|developmental stage:adult|tissue:muscle|genotype:wild type|age:adult fish", "adult muscle 2", "The flow cells were sequenced as 50\u00d72 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS Sequencing Kit version 3 and HCS version 2.0.12 data collection software. Raw RNA seq reads were aligned to the zebrafish genome assembly Zv9 for each sample using the Ensembl annotation Zv9 Danio rerio.Zv9.79.gtf by TopHat Version 2.0.12 . Each transcriptome was assembled by Cufflinks Version 2.2.1 . FPKM Fragments Per Kilobase of transcript per Million mapped reads was calculated using a protocol from Cufflinks. Isoform exp.diff was the result form Cuffdiff script and isoforms.fpkm table was the result from Cuffnorm script. Genome build: Zv9", "zebrafish adult muscle", null, "Tissues were homogenized using a mortar and pestle Fisher Scientific and total RNA was extracted using TRIzol Sigma according to the manufacturer\u2019s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument Agilent Technologies in the Mayo DNA sequencing core facility. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "developmental stage:adult|tissue:muscle|genotype:wild type|age:adult fish", "GSM2266462", "GSM2266462: adult muscle 2; Danio rerio; RNA Seq", "GSM2266462", null, "1", "Tissues were homogenized using a mortar and pestle Fisher Scientific and total RNA was extracted using TRIzol Sigma according to the manufacturer\u2019s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument Agilent Technologies in the Mayo DNA sequencing core facility. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2266462", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP081209", null, null, "adult_muscle-3.FCD29WDACXX_L8_IGATCAG.bam.R1.fastq.gz adult_muscle-3.FCD29WDACXX_L8_IGATCAG.bam.R2.fastq.gz", "fastq fastq", 6743529876.0, 66113038.0, "GSM2266462 r1", "0:51 1:51", "A:1704399315;C:1690169201;G:1644553844;T:1704276357;N:131159", 51, 51, null, null, 1704399315, 1690169201, 1644553844, 1704276357, 131159, "SRX2011209", "SRS1608493", "SRA451066", "GEO", "University of Maryland", 2, 0.94854, 0.94874, 0.06461, 0.06454, 0.80531, 0.80661, 0.49157, 0.49147, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-08-10", "Adult", "Adult", "Muscle", "Muscular System"], [41254, "SRR4017374", "SRX2011208", "SRS1608497", "SRP081209", "PRJNA338400", "Systematic identification and characterization of long non coding RNAs in zebrafish through RNA Seq", "GSE85416", "Transcriptome Analysis", "We sequenced mRNA from embryonic heart of zebrafish larvae 4 dpf adult heart of 6 mpf WIK fish and adult muscle of adult fish consisting of both fast twitch and slow twitch fibers. Overall design: Examination of mRNA and long noncoding RNA levels in embryonic heart adult heart and adult muscle tissues", null, "pubmed:28455512", null, "adult muscle 1", "GSM2266461", null, "source name:zebrafish adult muscle|developmental stage:adult|tissue:muscle|genotype:wild type|age:adult fish", "adult muscle 1", "The flow cells were sequenced as 50\u00d72 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS Sequencing Kit version 3 and HCS version 2.0.12 data collection software. Raw RNA seq reads were aligned to the zebrafish genome assembly Zv9 for each sample using the Ensembl annotation Zv9 Danio rerio.Zv9.79.gtf by TopHat Version 2.0.12 . Each transcriptome was assembled by Cufflinks Version 2.2.1 . FPKM Fragments Per Kilobase of transcript per Million mapped reads was calculated using a protocol from Cufflinks. Isoform exp.diff was the result form Cuffdiff script and isoforms.fpkm table was the result from Cuffnorm script. Genome build: Zv9", "zebrafish adult muscle", null, "Tissues were homogenized using a mortar and pestle Fisher Scientific and total RNA was extracted using TRIzol Sigma according to the manufacturer\u2019s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument Agilent Technologies in the Mayo DNA sequencing core facility. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "developmental stage:adult|tissue:muscle|genotype:wild type|age:adult fish", "GSM2266461", "GSM2266461: adult muscle 1; Danio rerio; RNA Seq", "GSM2266461", null, "1", "Tissues were homogenized using a mortar and pestle Fisher Scientific and total RNA was extracted using TRIzol Sigma according to the manufacturer\u2019s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument Agilent Technologies in the Mayo DNA sequencing core facility. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2266461", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP081209", null, null, "adult_muscle-2.FCD29WDACXX_L7_IACTTGA.bam.R2.fastq.gz adult_muscle-2.FCD29WDACXX_L7_IACTTGA.bam.R1.fastq.gz", "fastq fastq", 7874148264.0, 77197532.0, "GSM2266461 r1", "0:51 1:51", "A:1999194381;C:1965058509;G:1913030791;T:1996705765;N:158818", 51, 51, null, null, 1999194381, 1965058509, 1913030791, 1996705765, 158818, "SRX2011208", "SRS1608497", "SRA451066", "GEO", "University of Maryland", 2, 0.95199, 0.95135, 0.05873, 0.05869, 0.79711, 0.79754, 0.48769, 0.47024, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-08-10", "Adult", "Adult", "Muscle", "Muscular System"], [41255, "SRR4017373", "SRX2011207", "SRS1608495", "SRP081209", "PRJNA338400", "Systematic identification and characterization of long non coding RNAs in zebrafish through RNA Seq", "GSE85416", "Transcriptome Analysis", "We sequenced mRNA from embryonic heart of zebrafish larvae 4 dpf adult heart of 6 mpf WIK fish and adult muscle of adult fish consisting of both fast twitch and slow twitch fibers. Overall design: Examination of mRNA and long noncoding RNA levels in embryonic heart adult heart and adult muscle tissues", null, "pubmed:28455512", null, "adult muscle 0", "GSM2266460", null, "source name:zebrafish adult muscle|developmental stage:adult|tissue:muscle|genotype:wild type|age:adult fish", "adult muscle 0", "The flow cells were sequenced as 50\u00d72 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS Sequencing Kit version 3 and HCS version 2.0.12 data collection software. Raw RNA seq reads were aligned to the zebrafish genome assembly Zv9 for each sample using the Ensembl annotation Zv9 Danio rerio.Zv9.79.gtf by TopHat Version 2.0.12 . Each transcriptome was assembled by Cufflinks Version 2.2.1 . FPKM Fragments Per Kilobase of transcript per Million mapped reads was calculated using a protocol from Cufflinks. Isoform exp.diff was the result form Cuffdiff script and isoforms.fpkm table was the result from Cuffnorm script. Genome build: Zv9", "zebrafish adult muscle", null, "Tissues were homogenized using a mortar and pestle Fisher Scientific and total RNA was extracted using TRIzol Sigma according to the manufacturer\u2019s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument Agilent Technologies in the Mayo DNA sequencing core facility. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "developmental stage:adult|tissue:muscle|genotype:wild type|age:adult fish", "GSM2266460", "GSM2266460: adult muscle 0; Danio rerio; RNA Seq", "GSM2266460", null, "1", "Tissues were homogenized using a mortar and pestle Fisher Scientific and total RNA was extracted using TRIzol Sigma according to the manufacturer\u2019s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument Agilent Technologies in the Mayo DNA sequencing core facility. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2266460", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP081209", null, null, "adult_muscle-1.FCD29WDACXX_L6_ICAGATC.bam.R2.fastq.gz adult_muscle-1.FCD29WDACXX_L6_ICAGATC.bam.R1.fastq.gz", "fastq fastq", 8156140932.0, 79962166.0, "GSM2266460 r1", "0:51 1:51", "A:2067816702;C:2033763618;G:1988278323;T:2066053253;N:229036", 51, 51, null, null, 2067816702, 2033763618, 1988278323, 2066053253, 229036, "SRX2011207", "SRS1608495", "SRA451066", "GEO", "University of Maryland", 2, 0.94721, 0.94719, 0.06346, 0.06353, 0.79105, 0.79115, 0.50078, 0.50374, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-08-10", "Adult", "Adult", "Muscle", "Muscular System"], [44936, "SRR6308294", "SRX3408678", "SRS2701474", "SRP125291", "PRJNA419036", "Danio rerio strain:ASWT Transcriptome or Gene expression", "PRJNA419036", "Other", "A genome wide map of circular RNA in adult zebrafish.", null, null, null, "Zf muscle", "Zf muscle", null, "strain:ASWT|age:1year|sex:male|tissue:Muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "A genome wide map of circular RNA in adult zebrafish", "Zf muscle", "Zf muscle", "Tissue were isolated from adult zebrafish anaesthetized using 0.004% Tricaine Sigma USA. Extreme care was taken to avoid contamination to obtain pure homogenous tissue samples. The tissues were repeatedly washed in PBS to remove contaminating debris. The tissue samples were homogenized in Trizol for cell lysis Invitrogen USA. RNA was isolated from the homogenized tissue samples using RNeasy kit Qiagen USA. Sample preparation for sequencing was carried out using Truseq stranded RNA sample preparation kit Illumina USA as per supplier's instructions. In order to remove the ribosomal RNA rRNA one microgram of total RNA was hybridised with Ribo zero gold rRNA removal probe. Upon removing rRNA the samples were processed for fragmentation in the presence of ionic cations at 37 degree Celcius. First stranded complementary DNA cDNA was prepared by random hexamers and superscript II reverse transcriptase Invitrogen USA in presence of Actinomycin D to facilitate RNA dependent synthesis for improving strand specificity. The second strand was synthesised with second strand cDNA mix containing dUTP instead of dTTP and subjected to A base addition followed by adapter ligation. Final libraries were prepared by amplifying adapter ligated double strand cDNA. Clusters were generated on Hiseq flow cell v3 Illumina in cBot according to standard protocol Illumina USA.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP125291", null, null, "Zf_muscle_R1.fastq Zf_muscle_R2.fastq", "fastq fastq", 3777044386.0, 20362229.0, "Zf muscle R1.fastq", "0:97.14 1:88.35", "A:948171837;C:941487080;G:936414216;T:950742547;N:228706", 97, 88, null, null, 948171837, 941487080, 936414216, 950742547, 228706, "SRX3408678", "SRS2701474", "SRA631861", "CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.94043, 0.955, 0.22684, 0.2231, 0.77222, 0.77368, 0.63355, 0.63196, 101, 93, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "India", "2017-11-20", "Adult", "Adult", "Muscle", "Muscular System"], [48062, "SRR7008299", "SRX3940787", "SRS3171588", "SRP140471", "PRJNA450343", "A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways", "GSE113169", "Transcriptome Analysis", "Acromegaly is a pathological condition due to excess growth hormone GH secretion. Acromegaly patients exhibit a deterioration of health and many associated complications such as cardiovascular issues arthritis kidney diseases muscular weakness and colon cancer. Since these complications are generalized throughout the body we investigated the effect of GH excess on cellular integrity. Here we established stable acromegaly model zebrafish lines that overexpress tilapia GH and the red fluorescence protein RFP reporter gene for tracking GH gene expression throughout generations and performed RNA Seq data analysis from different organs. Intriguingly heatmap and Expression2Kinases X2K analysis revealed the enrichment of DNA damage markers in various organs. Moreover H2A.X immunostaining analysis in acromegaly zebrafish larvae and the adult acromegaly model brain and muscle showed a robust increase in the number of DNA damaged cells. Using Gene Set Enrichment Analysis GSEA we found that the acromegaly zebrafish model had impaired DNA repair pathways in the liver such as double strand break DSB homologous recombination repair HRR non homologous end joining NHEJ nucleotide excision repair NER and translesion synthesis TLS. Interestingly the impairment of DNA repair was even more prominent in acromegaly model than in aged zebrafish three years old. Thus our study demonstrates that affection of cellular integrity is characteristic of acromegaly Overall design: Total mRNA obtained from 1 years old acromegaly zebrafish model muscle brain kidney liver and 3 dpf larvae compared to wild type WT zebrafish were generated by deep sequencing using Illumina.", null, "pubmed:30336646;pubmed:32517323;pubmed:33849304", null, "Muscle WT rep3", "GSM3098435", null, "source name:Muscle|genotype:wild type|tissue:Muscle|age:1 year old", "Muscle WT rep3", "Illumina Casava1.7 software used for basecalling. HISAT2 software was used according to the instructions from the program designers to map the raw reads of acromegaly and WT samples to zebrafish genome reference GRCz10 retrieved from Ensembl database together with the annotation file. The Cufflinks pipeline was used to assign reads to known transcripts and test for differential expression between acromegaly model and the WT samples. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads FPKM. Genome build: GRCz10 Supplementary files format and content: One tab delimited text file containing all FPKM values for all Samples.", "Muscle", null, "tissues were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", null, "genotype:wild type|tissue:Muscle|age:1 year old", "GSM3098435", "GSM3098435: Muscle WT rep3; Danio rerio; RNA Seq", "GSM3098435", null, "1", "tissues were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", "GEO Accession:GSM3098435", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP140471", null, null, "WT_M6_Muscle_14_2.fq.gz WT_M6_Muscle_14_1.fq.gz", "fastq fastq", 1243422200.0, 6217111.0, "GSM3098435 r1", "0:100 1:100", "A:325766031;C:296285050;G:292596318;T:328586492;N:188309", 100, 100, null, null, 325766031, 296285050, 292596318, 328586492, 188309, "SRX3940787", "SRS3171588", "SRA690975", "GEO", "Aquatic Molecular Biology and Biotechnology, Aquatic Bioscience, The University of Tokyo", 2, 0.96604, 0.96675, 0.03881, 0.0371, 0.80758, 0.80779, 0.5744, 0.52029, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-04-16", "Adult", "Adult", "Muscle", "Muscular System"], [48063, "SRR7008298", "SRX3940786", "SRS3171587", "SRP140471", "PRJNA450343", "A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways", "GSE113169", "Transcriptome Analysis", "Acromegaly is a pathological condition due to excess growth hormone GH secretion. Acromegaly patients exhibit a deterioration of health and many associated complications such as cardiovascular issues arthritis kidney diseases muscular weakness and colon cancer. Since these complications are generalized throughout the body we investigated the effect of GH excess on cellular integrity. Here we established stable acromegaly model zebrafish lines that overexpress tilapia GH and the red fluorescence protein RFP reporter gene for tracking GH gene expression throughout generations and performed RNA Seq data analysis from different organs. Intriguingly heatmap and Expression2Kinases X2K analysis revealed the enrichment of DNA damage markers in various organs. Moreover H2A.X immunostaining analysis in acromegaly zebrafish larvae and the adult acromegaly model brain and muscle showed a robust increase in the number of DNA damaged cells. Using Gene Set Enrichment Analysis GSEA we found that the acromegaly zebrafish model had impaired DNA repair pathways in the liver such as double strand break DSB homologous recombination repair HRR non homologous end joining NHEJ nucleotide excision repair NER and translesion synthesis TLS. Interestingly the impairment of DNA repair was even more prominent in acromegaly model than in aged zebrafish three years old. Thus our study demonstrates that affection of cellular integrity is characteristic of acromegaly Overall design: Total mRNA obtained from 1 years old acromegaly zebrafish model muscle brain kidney liver and 3 dpf larvae compared to wild type WT zebrafish were generated by deep sequencing using Illumina.", null, "pubmed:30336646;pubmed:32517323;pubmed:33849304", null, "Muscle WT rep2", "GSM3098434", null, "source name:Muscle|genotype:wild type|tissue:Muscle|age:1 year old", "Muscle WT rep2", "Illumina Casava1.7 software used for basecalling. HISAT2 software was used according to the instructions from the program designers to map the raw reads of acromegaly and WT samples to zebrafish genome reference GRCz10 retrieved from Ensembl database together with the annotation file. The Cufflinks pipeline was used to assign reads to known transcripts and test for differential expression between acromegaly model and the WT samples. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads FPKM. Genome build: GRCz10 Supplementary files format and content: One tab delimited text file containing all FPKM values for all Samples.", "Muscle", null, "tissues were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", null, "genotype:wild type|tissue:Muscle|age:1 year old", "GSM3098434", "GSM3098434: Muscle WT rep2; Danio rerio; RNA Seq", "GSM3098434", null, "1", "tissues were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", "GEO Accession:GSM3098434", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP140471", null, null, "WT_M5_Muscle_13_1.fq.gz WT_M5_Muscle_13_2.fq.gz", "fastq fastq", 1386324600.0, 6931623.0, "GSM3098434 r1", "0:100 1:100", "A:359710957;C:333924985;G:328821373;T:363654803;N:212482", 100, 100, null, null, 359710957, 333924985, 328821373, 363654803, 212482, "SRX3940786", "SRS3171587", "SRA690975", "GEO", "Aquatic Molecular Biology and Biotechnology, Aquatic Bioscience, The University of Tokyo", 2, 0.96338, 0.96384, 0.04312, 0.04169, 0.79383, 0.79555, 0.50865, 0.54488, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-04-16", "Adult", "Adult", "Muscle", "Muscular System"], [48064, "SRR7008297", "SRX3940785", "SRS3171586", "SRP140471", "PRJNA450343", "A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways", "GSE113169", "Transcriptome Analysis", "Acromegaly is a pathological condition due to excess growth hormone GH secretion. Acromegaly patients exhibit a deterioration of health and many associated complications such as cardiovascular issues arthritis kidney diseases muscular weakness and colon cancer. Since these complications are generalized throughout the body we investigated the effect of GH excess on cellular integrity. Here we established stable acromegaly model zebrafish lines that overexpress tilapia GH and the red fluorescence protein RFP reporter gene for tracking GH gene expression throughout generations and performed RNA Seq data analysis from different organs. Intriguingly heatmap and Expression2Kinases X2K analysis revealed the enrichment of DNA damage markers in various organs. Moreover H2A.X immunostaining analysis in acromegaly zebrafish larvae and the adult acromegaly model brain and muscle showed a robust increase in the number of DNA damaged cells. Using Gene Set Enrichment Analysis GSEA we found that the acromegaly zebrafish model had impaired DNA repair pathways in the liver such as double strand break DSB homologous recombination repair HRR non homologous end joining NHEJ nucleotide excision repair NER and translesion synthesis TLS. Interestingly the impairment of DNA repair was even more prominent in acromegaly model than in aged zebrafish three years old. Thus our study demonstrates that affection of cellular integrity is characteristic of acromegaly Overall design: Total mRNA obtained from 1 years old acromegaly zebrafish model muscle brain kidney liver and 3 dpf larvae compared to wild type WT zebrafish were generated by deep sequencing using Illumina.", null, "pubmed:30336646;pubmed:32517323;pubmed:33849304", null, "Muscle WT rep1", "GSM3098433", null, "source name:Muscle|genotype:wild type|tissue:Muscle|age:1 year old", "Muscle WT rep1", "Illumina Casava1.7 software used for basecalling. HISAT2 software was used according to the instructions from the program designers to map the raw reads of acromegaly and WT samples to zebrafish genome reference GRCz10 retrieved from Ensembl database together with the annotation file. The Cufflinks pipeline was used to assign reads to known transcripts and test for differential expression between acromegaly model and the WT samples. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads FPKM. Genome build: GRCz10 Supplementary files format and content: One tab delimited text file containing all FPKM values for all Samples.", "Muscle", null, "tissues were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", null, "genotype:wild type|tissue:Muscle|age:1 year old", "GSM3098433", "GSM3098433: Muscle WT rep1; Danio rerio; RNA Seq", "GSM3098433", null, "1", "tissues were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", "GEO Accession:GSM3098433", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP140471", null, null, "WT_M4_Muscle_12_2.fq.gz WT_M4_Muscle_12_1.fq.gz", "fastq fastq", 1088840400.0, 5444202.0, "GSM3098433 r1", "0:100 1:100", "A:289051296;C:255664310;G:251957997;T:292000634;N:166163", 100, 100, null, null, 289051296, 255664310, 251957997, 292000634, 166163, "SRX3940785", "SRS3171586", "SRA690975", "GEO", "Aquatic Molecular Biology and Biotechnology, Aquatic Bioscience, The University of Tokyo", 2, 0.9542, 0.95445, 0.05492, 0.05405, 0.75469, 0.7559, 0.48719, 0.56695, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-04-16", "Adult", "Adult", "Muscle", "Muscular System"], [48065, "SRR7008296", "SRX3940784", "SRS3171585", "SRP140471", "PRJNA450343", "A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways", "GSE113169", "Transcriptome Analysis", "Acromegaly is a pathological condition due to excess growth hormone GH secretion. Acromegaly patients exhibit a deterioration of health and many associated complications such as cardiovascular issues arthritis kidney diseases muscular weakness and colon cancer. Since these complications are generalized throughout the body we investigated the effect of GH excess on cellular integrity. Here we established stable acromegaly model zebrafish lines that overexpress tilapia GH and the red fluorescence protein RFP reporter gene for tracking GH gene expression throughout generations and performed RNA Seq data analysis from different organs. Intriguingly heatmap and Expression2Kinases X2K analysis revealed the enrichment of DNA damage markers in various organs. Moreover H2A.X immunostaining analysis in acromegaly zebrafish larvae and the adult acromegaly model brain and muscle showed a robust increase in the number of DNA damaged cells. Using Gene Set Enrichment Analysis GSEA we found that the acromegaly zebrafish model had impaired DNA repair pathways in the liver such as double strand break DSB homologous recombination repair HRR non homologous end joining NHEJ nucleotide excision repair NER and translesion synthesis TLS. Interestingly the impairment of DNA repair was even more prominent in acromegaly model than in aged zebrafish three years old. Thus our study demonstrates that affection of cellular integrity is characteristic of acromegaly Overall design: Total mRNA obtained from 1 years old acromegaly zebrafish model muscle brain kidney liver and 3 dpf larvae compared to wild type WT zebrafish were generated by deep sequencing using Illumina.", null, "pubmed:30336646;pubmed:32517323;pubmed:33849304", null, "Muscle ACRO rep3", "GSM3098432", null, "source name:Muscle|genotype:Acromegaly zebrafish model|tissue:Muscle|age:1 year old", "Muscle ACRO rep3", "Illumina Casava1.7 software used for basecalling. HISAT2 software was used according to the instructions from the program designers to map the raw reads of acromegaly and WT samples to zebrafish genome reference GRCz10 retrieved from Ensembl database together with the annotation file. The Cufflinks pipeline was used to assign reads to known transcripts and test for differential expression between acromegaly model and the WT samples. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads FPKM. Genome build: GRCz10 Supplementary files format and content: One tab delimited text file containing all FPKM values for all Samples.", "Muscle", null, "tissues were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", null, "genotype:Acromegaly zebrafish model|tissue:Muscle|age:1 year old", "GSM3098432", "GSM3098432: Muscle ACRO rep3; Danio rerio; RNA Seq", "GSM3098432", null, "1", "tissues were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", "GEO Accession:GSM3098432", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP140471", null, null, "GH_M3_Muscle_11_1.fq.gz GH_M3_Muscle_11_2.fq.gz", "fastq fastq", 1167772600.0, 5838863.0, "GSM3098432 r1", "0:100 1:100", "A:306351582;C:277684244;G:274694843;T:308864675;N:177256", 100, 100, null, null, 306351582, 277684244, 274694843, 308864675, 177256, "SRX3940784", "SRS3171585", "SRA690975", "GEO", "Aquatic Molecular Biology and Biotechnology, Aquatic Bioscience, The University of Tokyo", 2, 0.96344, 0.96466, 0.03591, 0.03516, 0.81211, 0.81333, 0.55949, 0.56695, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-04-16", "Adult", "Adult", "Muscle", "Muscular System"]], "truncated": false, "filtered_table_rows_count": 432, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, 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