{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Adult\" and experiment.library_selection = \"RANDOM PCR\"", "rows": [[44932, "SRR6308290", "SRX3408682", "SRS2701478", "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 gills", "Zf gills", null, "strain:ASWT|age:1year|sex:male|tissue:Gills|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "A genome wide map of circular RNA in adult zebrafish", "Zf gills", "Zf gills", "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. 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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. 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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. 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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. 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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"], [48033, "SRR6921815", "SRX3869077", "SRS3112052", "SRP136856", "PRJNA448207", "Transcriptomic profiles of zebrafish liver exposed to phenanthrene", "PRJNA448207", "Other", "The present study aims to examine the toxicological effects of phenanthrene in the molecular mechanism in zebrafish. We performed RNA Seq analysis on zebrafish liver responding to phenanthrene exposure. Genes involved in phenanthrene exposure to zebrafish liver were identified from the transcriptional data. This study provides the completed evaluation of toxic effect of phenanthrene exposure to zebrafish by transcriptional approaches. Our findings could present foundation for further study on molecular mechanism responsible for zebrafish's responses to phenanthrene exposure.", null, null, "Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L  and livers were sampled and pooled", null, "PHE3d.3", null, "strain:not applicable|isolate:not applicable|breed:AB line|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:Adult fish|sex:pooled male and female|tissue:liver|biomaterial provider:China Zebrafish Resource Center|birth location:Wuhan  China|breeding method:maintained in the semi static system under conditions of water quality and illumination as follows: temperature 2327   pH 78  dissolved oxygen concentration 5 mg   L 1  total hardness 10250 mg CaCO3 per liter  and light/dark period of 12:12 h.|genotype:AB line|health state:Healthy|sample type:tissue sample|treatment:Fish exposed to phenanthrene for xxx day at concentration of 300 g L 1|replicate:biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day", "PHE3d.3", "PHE3d.3", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP136856", null, null, "PHE3d_3_1.fq.gz PHE3d_3_2.fq.gz", "fastq fastq", 6871439400.0, 22904798.0, "PHE3d 3 1.fq.gz", "0:150 1:150", "A:1771640937;C:1661273097;G:1659191846;T:1774900542;N:4432978", 150, 150, null, null, 1771640937, 1661273097, 1659191846, 1774900542, 4432978, "SRX3869077", "SRS3112052", "SRA678027", "Pearl River Fisheries Research Institute, CAFS|Fisheries environmental protection laboratory", "Pearl River Fisheries Research Institute, CAFS", 2, 0.92605, 0.9282, 0.04717, 0.04722, 0.72606, 0.73421, 0.51267, 0.50362, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-03-31", "Adult", "Adult", "Liver", "Liver and Biliary System"], [48034, "SRR6921816", "SRX3869076", "SRS3112051", "SRP136856", "PRJNA448207", "Transcriptomic profiles of zebrafish liver exposed to phenanthrene", "PRJNA448207", "Other", "The present study aims to examine the toxicological effects of phenanthrene in the molecular mechanism in zebrafish. We performed RNA Seq analysis on zebrafish liver responding to phenanthrene exposure. Genes involved in phenanthrene exposure to zebrafish liver were identified from the transcriptional data. This study provides the completed evaluation of toxic effect of phenanthrene exposure to zebrafish by transcriptional approaches. Our findings could present foundation for further study on molecular mechanism responsible for zebrafish's responses to phenanthrene exposure.", null, null, "Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L  and livers were sampled and pooled", null, "PHE7d.1", null, "strain:not applicable|isolate:not applicable|breed:AB line|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:Adult fish|sex:pooled male and female|tissue:liver|biomaterial provider:China Zebrafish Resource Center|birth location:Wuhan  China|breeding method:maintained in the semi static system under conditions of water quality and illumination as follows: temperature 2327   pH 78  dissolved oxygen concentration 5 mg   L 1  total hardness 10250 mg CaCO3 per liter  and light/dark period of 12:12 h.|genotype:AB line|health state:Healthy|sample type:tissue sample|treatment:Fish exposed to phenanthrene for xxx day at concentration of 300 g L 1|replicate:biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day", "PHE7d.1", "PHE7d.1", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP136856", null, null, "PHE7d_1_2.fq.gz PHE7d_1_1.fq.gz", "fastq fastq", 7415333700.0, 24717779.0, "PHE7d 1 2.fq.gz", "0:150 1:150", "A:1926590053;C:1783903190;G:1780648419;T:1919390554;N:4801484", 150, 150, null, null, 1926590053, 1783903190, 1780648419, 1919390554, 4801484, "SRX3869076", "SRS3112051", "SRA678027", "Pearl River Fisheries Research Institute, CAFS|Fisheries environmental protection laboratory", "Pearl River Fisheries Research Institute, CAFS", 2, 0.94375, 0.94379, 0.03337, 0.03376, 0.77567, 0.78589, 0.36225, 0.3605, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-03-31", "Adult", "Adult", "Liver", "Liver and Biliary System"], [48035, "SRR6921817", "SRX3869075", "SRS3112050", "SRP136856", "PRJNA448207", "Transcriptomic profiles of zebrafish liver exposed to phenanthrene", "PRJNA448207", "Other", "The present study aims to examine the toxicological effects of phenanthrene in the molecular mechanism in zebrafish. We performed RNA Seq analysis on zebrafish liver responding to phenanthrene exposure. Genes involved in phenanthrene exposure to zebrafish liver were identified from the transcriptional data. This study provides the completed evaluation of toxic effect of phenanthrene exposure to zebrafish by transcriptional approaches. Our findings could present foundation for further study on molecular mechanism responsible for zebrafish's responses to phenanthrene exposure.", null, null, "Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L  and livers were sampled and pooled", null, "PHE1d.2", null, "strain:not applicable|isolate:not applicable|breed:AB line|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:Adult fish|sex:pooled male and female|tissue:liver|biomaterial provider:China Zebrafish Resource Center|birth location:Wuhan  China|breeding method:maintained in the semi static system under conditions of water quality and illumination as follows: temperature 2327   pH 78  dissolved oxygen concentration 5 mg   L 1  total hardness 10250 mg CaCO3 per liter  and light/dark period of 12:12 h.|genotype:AB line|health state:Healthy|sample type:tissue sample|treatment:Fish exposed to phenanthrene for xxx day at concentration of 300 g L 1|replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day", "PHE1d.2", "PHE1d.2", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP136856", null, null, "PHE1d_2_1.fq.gz PHE1d_2_2.fq.gz", "fastq fastq", 6652993800.0, 22176646.0, "PHE1d 2 2.fq.gz", "0:150 1:150", "A:1711396541;C:1615315487;G:1608586740;T:1713390744;N:4304288", 150, 150, null, null, 1711396541, 1615315487, 1608586740, 1713390744, 4304288, "SRX3869075", "SRS3112050", "SRA678027", "Pearl River Fisheries Research Institute, CAFS|Fisheries environmental protection laboratory", "Pearl River Fisheries Research Institute, CAFS", 2, 0.92873, 0.93082, 0.0516, 0.05127, 0.72667, 0.73572, 0.51365, 0.53418, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-03-31", "Adult", "Adult", "Liver", "Liver and Biliary System"], [48036, "SRR6921818", "SRX3869074", "SRS3112049", "SRP136856", "PRJNA448207", "Transcriptomic profiles of zebrafish liver exposed to phenanthrene", "PRJNA448207", "Other", "The present study aims to examine the toxicological effects of phenanthrene in the molecular mechanism in zebrafish. We performed RNA Seq analysis on zebrafish liver responding to phenanthrene exposure. Genes involved in phenanthrene exposure to zebrafish liver were identified from the transcriptional data. This study provides the completed evaluation of toxic effect of phenanthrene exposure to zebrafish by transcriptional approaches. Our findings could present foundation for further study on molecular mechanism responsible for zebrafish's responses to phenanthrene exposure.", null, null, "Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L  and livers were sampled and pooled", null, "PHE1d.3", null, "strain:not applicable|isolate:not applicable|breed:AB line|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:Adult fish|sex:pooled male and female|tissue:liver|biomaterial provider:China Zebrafish Resource Center|birth location:Wuhan  China|breeding method:maintained in the semi static system under conditions of water quality and illumination as follows: temperature 2327   pH 78  dissolved oxygen concentration 5 mg   L 1  total hardness 10250 mg CaCO3 per liter  and light/dark period of 12:12 h.|genotype:AB line|health state:Healthy|sample type:tissue sample|treatment:Fish exposed to phenanthrene for xxx day at concentration of 300 g L 1|replicate:biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day", "PHE1d.3", "PHE1d.3", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP136856", null, null, "PHE1d_3_2.fq.gz PHE1d_3_1.fq.gz", "fastq fastq", 7348663800.0, 24495546.0, "PHE1d 3 2.fq.gz", "0:150 1:150", "A:1883497210;C:1789041904;G:1790415614;T:1880946063;N:4763009", 150, 150, null, null, 1883497210, 1789041904, 1790415614, 1880946063, 4763009, "SRX3869074", "SRS3112049", "SRA678027", "Pearl River Fisheries Research Institute, CAFS|Fisheries environmental protection laboratory", "Pearl River Fisheries Research Institute, CAFS", 2, 0.93797, 0.94003, 0.02784, 0.02766, 0.74576, 0.75457, 0.39126, 0.40303, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-03-31", "Adult", "Adult", "Liver", "Liver and Biliary System"], [48037, "SRR6921819", "SRX3869073", "SRS3112048", "SRP136856", "PRJNA448207", "Transcriptomic profiles of zebrafish liver exposed to phenanthrene", "PRJNA448207", "Other", "The present study aims to examine the toxicological effects of phenanthrene in the molecular mechanism in zebrafish. We performed RNA Seq analysis on zebrafish liver responding to phenanthrene exposure. Genes involved in phenanthrene exposure to zebrafish liver were identified from the transcriptional data. This study provides the completed evaluation of toxic effect of phenanthrene exposure to zebrafish by transcriptional approaches. Our findings could present foundation for further study on molecular mechanism responsible for zebrafish's responses to phenanthrene exposure.", null, null, "Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L  and livers were sampled and pooled", null, "PHE3d.1", null, "strain:not applicable|isolate:not applicable|breed:AB line|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:Adult fish|sex:pooled male and female|tissue:liver|biomaterial provider:China Zebrafish Resource Center|birth location:Wuhan  China|breeding method:maintained in the semi static system under conditions of water quality and illumination as follows: temperature 2327   pH 78  dissolved oxygen concentration 5 mg   L 1  total hardness 10250 mg CaCO3 per liter  and light/dark period of 12:12 h.|genotype:AB line|health state:Healthy|sample type:tissue sample|treatment:Fish exposed to phenanthrene for xxx day at concentration of 300 g L 1|replicate:biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day", "PHE3d.1", "PHE3d.1", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP136856", null, null, "PHE3d_1_2.fq.gz PHE3d_1_1.fq.gz", "fastq fastq", 7891468200.0, 26304894.0, "PHE3d 1 2.fq.gz", "0:150 1:150", "A:2050227199;C:1895557315;G:1895981666;T:2044562188;N:5139832", 150, 150, null, null, 2050227199, 1895557315, 1895981666, 2044562188, 5139832, "SRX3869073", "SRS3112048", "SRA678027", "Pearl River Fisheries Research Institute, CAFS|Fisheries environmental protection laboratory", "Pearl River Fisheries Research Institute, CAFS", 2, 0.93444, 0.93434, 0.01928, 0.01936, 0.74789, 0.75803, 0.38181, 0.39248, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-03-31", "Adult", "Adult", "Liver", "Liver and Biliary System"], [48038, "SRR6921820", "SRX3869072", "SRS3112047", "SRP136856", "PRJNA448207", "Transcriptomic profiles of zebrafish liver exposed to phenanthrene", "PRJNA448207", "Other", "The present study aims to examine the toxicological effects of phenanthrene in the molecular mechanism in zebrafish. We performed RNA Seq analysis on zebrafish liver responding to phenanthrene exposure. Genes involved in phenanthrene exposure to zebrafish liver were identified from the transcriptional data. This study provides the completed evaluation of toxic effect of phenanthrene exposure to zebrafish by transcriptional approaches. Our findings could present foundation for further study on molecular mechanism responsible for zebrafish's responses to phenanthrene exposure.", null, null, "Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L  and livers were sampled and pooled", null, "PHE3d.2", null, "strain:not applicable|isolate:not applicable|breed:AB line|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:Adult fish|sex:pooled male and female|tissue:liver|biomaterial provider:China Zebrafish Resource Center|birth location:Wuhan  China|breeding method:maintained in the semi static system under conditions of water quality and illumination as follows: temperature 2327   pH 78  dissolved oxygen concentration 5 mg   L 1  total hardness 10250 mg CaCO3 per liter  and light/dark period of 12:12 h.|genotype:AB line|health state:Healthy|sample type:tissue sample|treatment:Fish exposed to phenanthrene for xxx day at concentration of 300 g L 1|replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day", "PHE3d.2", "PHE3d.2", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP136856", null, null, "PHE3d_2_1.fq.gz PHE3d_2_2.fq.gz", "fastq fastq", 8406789300.0, 28022631.0, "PHE3d 2 1.fq.gz", "0:150 1:150", "A:2187414004;C:2019038004;G:2013512837;T:2181333490;N:5490965", 150, 150, null, null, 2187414004, 2019038004, 2013512837, 2181333490, 5490965, "SRX3869072", "SRS3112047", "SRA678027", "Pearl River Fisheries Research Institute, CAFS|Fisheries environmental protection laboratory", "Pearl River Fisheries Research Institute, CAFS", 2, 0.91151, 0.91449, 0.01671, 0.017, 0.75315, 0.76203, 0.46837, 0.47419, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-03-31", "Adult", "Adult", "Liver", "Liver and Biliary System"], [48039, "SRR6921821", "SRX3869071", "SRS3112046", "SRP136856", "PRJNA448207", "Transcriptomic profiles of zebrafish liver exposed to phenanthrene", "PRJNA448207", "Other", "The present study aims to examine the toxicological effects of phenanthrene in the molecular mechanism in zebrafish. We performed RNA Seq analysis on zebrafish liver responding to phenanthrene exposure. Genes involved in phenanthrene exposure to zebrafish liver were identified from the transcriptional data. This study provides the completed evaluation of toxic effect of phenanthrene exposure to zebrafish by transcriptional approaches. 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We performed RNA Seq analysis on zebrafish liver responding to phenanthrene exposure. Genes involved in phenanthrene exposure to zebrafish liver were identified from the transcriptional data. This study provides the completed evaluation of toxic effect of phenanthrene exposure to zebrafish by transcriptional approaches. 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We performed RNA Seq analysis on zebrafish liver responding to phenanthrene exposure. Genes involved in phenanthrene exposure to zebrafish liver were identified from the transcriptional data. This study provides the completed evaluation of toxic effect of phenanthrene exposure to zebrafish by transcriptional approaches. Our findings could present foundation for further study on molecular mechanism responsible for zebrafish's responses to phenanthrene exposure.", null, null, "Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L  and livers were sampled and pooled", null, "PHE0d.3", null, "strain:not applicable|isolate:not applicable|breed:AB line|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:Adult fish|sex:pooled male and female|tissue:liver|biomaterial provider:China Zebrafish Resource Center|birth location:Wuhan  China|breeding method:maintained in the semi static system under conditions of water quality and illumination as follows: temperature 2327   pH 78  dissolved oxygen concentration 5 mg   L 1  total hardness 10250 mg CaCO3 per liter  and light/dark period of 12:12 h.|genotype:AB line|health state:Healthy|sample type:tissue sample|treatment:Fish maintained without xxx exposure|replicate:biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult male and female without xxx exposure", "PHE0d.3", "PHE0d.3", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP136856", null, null, "PHE0d_3_2.fq.gz", "fastq", 3650312550.0, 24335417.0, "PHE0d 3 2.fq.gz", "0:0 1:150", "A:945286124;C:876624311;G:880379003;T:946003595;N:2019517", 0, 150, null, null, 945286124, 876624311, 880379003, 946003595, 2019517, "SRX3869069", "SRS3112044", "SRA678027", "Pearl River Fisheries Research Institute, CAFS|Fisheries environmental protection laboratory", "Pearl River Fisheries Research Institute, CAFS", 1, 0.93747, null, 0.0274, null, 0.76031, null, 0.35099, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-03-31", "Adult", "Adult", "Liver", "Liver and Biliary System"], [48042, "SRR6921824", "SRX3869068", "SRS3112043", "SRP136856", "PRJNA448207", "Transcriptomic profiles of zebrafish liver exposed to phenanthrene", "PRJNA448207", "Other", "The present study aims to examine the toxicological effects of phenanthrene in the molecular mechanism in zebrafish. We performed RNA Seq analysis on zebrafish liver responding to phenanthrene exposure. Genes involved in phenanthrene exposure to zebrafish liver were identified from the transcriptional data. This study provides the completed evaluation of toxic effect of phenanthrene exposure to zebrafish by transcriptional approaches. Our findings could present foundation for further study on molecular mechanism responsible for zebrafish's responses to phenanthrene exposure.", null, null, "Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L  and livers were sampled and pooled", null, "PHE1d.1", null, "strain:not applicable|isolate:not applicable|breed:AB line|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:Adult fish|sex:pooled male and female|tissue:liver|biomaterial provider:China Zebrafish Resource Center|birth location:Wuhan  China|breeding method:maintained in the semi static system under conditions of water quality and illumination as follows: temperature 2327   pH 78  dissolved oxygen concentration 5 mg   L 1  total hardness 10250 mg CaCO3 per liter  and light/dark period of 12:12 h.|genotype:AB line|health state:Healthy|sample type:tissue sample|treatment:Fish exposed to phenanthrene for xxx day at concentration of 300 g L 1|replicate:biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day", "PHE1d.1", "PHE1d.1", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP136856", null, null, "PHE1d_1_1.fq.gz PHE1d_1_2.fq.gz", "fastq fastq", 7353145800.0, 24510486.0, "PHE1d 1 1.fq.gz", "0:150 1:150", "A:1896735212;C:1783435525;G:1779850974;T:1888352720;N:4771369", 150, 150, null, null, 1896735212, 1783435525, 1779850974, 1888352720, 4771369, "SRX3869068", "SRS3112043", "SRA678027", "Pearl River Fisheries Research Institute, CAFS|Fisheries environmental protection laboratory", "Pearl River Fisheries Research Institute, CAFS", 2, 0.9244, 0.92601, 0.01781, 0.01775, 0.74884, 0.75507, 0.43251, 0.44499, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-03-31", "Adult", "Adult", "Liver", "Liver and Biliary System"], [48043, "SRR6921825", "SRX3869067", "SRS3112042", "SRP136856", "PRJNA448207", "Transcriptomic profiles of zebrafish liver exposed to phenanthrene", "PRJNA448207", "Other", "The present study aims to examine the toxicological effects of phenanthrene in the molecular mechanism in zebrafish. We performed RNA Seq analysis on zebrafish liver responding to phenanthrene exposure. Genes involved in phenanthrene exposure to zebrafish liver were identified from the transcriptional data. This study provides the completed evaluation of toxic effect of phenanthrene exposure to zebrafish by transcriptional approaches. Our findings could present foundation for further study on molecular mechanism responsible for zebrafish's responses to phenanthrene exposure.", null, null, "Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L  and livers were sampled and pooled", null, "PHE7d.2", null, "strain:not applicable|isolate:not applicable|breed:AB line|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:Adult fish|sex:pooled male and female|tissue:liver|biomaterial provider:China Zebrafish Resource Center|birth location:Wuhan  China|breeding method:maintained in the semi static system under conditions of water quality and illumination as follows: temperature 2327   pH 78  dissolved oxygen concentration 5 mg   L 1  total hardness 10250 mg CaCO3 per liter  and light/dark period of 12:12 h.|genotype:AB line|health state:Healthy|sample type:tissue sample|treatment:Fish exposed to phenanthrene for xxx day at concentration of 300 g L 1|replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day", "PHE7d.2", "PHE7d.2", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP136856", null, null, "PHE7d_2_1.fq.gz PHE7d_2_2.fq.gz", "fastq fastq", 7224224100.0, 24080747.0, "PHE7d 2 1.fq.gz", "0:150 1:150", "A:1825676690;C:1788393328;G:1782936749;T:1822524668;N:4692665", 150, 150, null, null, 1825676690, 1788393328, 1782936749, 1822524668, 4692665, "SRX3869067", "SRS3112042", "SRA678027", "Pearl River Fisheries Research Institute, CAFS|Fisheries environmental protection laboratory", "Pearl River Fisheries Research Institute, CAFS", 2, 0.9373, 0.9391, 0.05048, 0.05061, 0.75939, 0.76917, 0.47799, 0.50408, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-03-31", "Adult", "Adult", "Liver", "Liver and Biliary System"], [48044, "SRR6921826", "SRX3869066", "SRS3112041", "SRP136856", "PRJNA448207", "Transcriptomic profiles of zebrafish liver exposed to phenanthrene", "PRJNA448207", "Other", "The present study aims to examine the toxicological effects of phenanthrene in the molecular mechanism in zebrafish. We performed RNA Seq analysis on zebrafish liver responding to phenanthrene exposure. Genes involved in phenanthrene exposure to zebrafish liver were identified from the transcriptional data. This study provides the completed evaluation of toxic effect of phenanthrene exposure to zebrafish by transcriptional approaches. Our findings could present foundation for further study on molecular mechanism responsible for zebrafish's responses to phenanthrene exposure.", null, null, "Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L  and livers were sampled and pooled", null, "PHE7d.3", null, "strain:not applicable|isolate:not applicable|breed:AB line|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:Adult fish|sex:pooled male and female|tissue:liver|biomaterial provider:China Zebrafish Resource Center|birth location:Wuhan  China|breeding method:maintained in the semi static system under conditions of water quality and illumination as follows: temperature 2327   pH 78  dissolved oxygen concentration 5 mg   L 1  total hardness 10250 mg CaCO3 per liter  and light/dark period of 12:12 h.|genotype:AB line|health state:Healthy|sample type:tissue sample|treatment:Fish exposed to phenanthrene for xxx day at concentration of 300 g L 1|replicate:biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day", "PHE7d.3", "PHE7d.3", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP136856", null, null, "PHE7d_3_1.fq.gz PHE7d_3_2.fq.gz", "fastq fastq", 7251597900.0, 24171993.0, "PHE7d 3 1.fq.gz", "0:150 1:150", "A:1868321462;C:1755689716;G:1756761060;T:1866130827;N:4694835", 150, 150, null, null, 1868321462, 1755689716, 1756761060, 1866130827, 4694835, "SRX3869066", "SRS3112041", "SRA678027", "Pearl River Fisheries Research Institute, CAFS|Fisheries environmental protection laboratory", "Pearl River Fisheries Research Institute, CAFS", 2, 0.92489, 0.9282, 0.04608, 0.04554, 0.74961, 0.75814, 0.52555, 0.53342, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-03-31", "Adult", "Adult", "Liver", "Liver and Biliary System"], [48045, "SRR6921827", "SRX3869065", "SRS3112040", "SRP136856", "PRJNA448207", "Transcriptomic profiles of zebrafish liver exposed to phenanthrene", "PRJNA448207", "Other", "The present study aims to examine the toxicological effects of phenanthrene in the molecular mechanism in zebrafish. We performed RNA Seq analysis on zebrafish liver responding to phenanthrene exposure. Genes involved in phenanthrene exposure to zebrafish liver were identified from the transcriptional data. This study provides the completed evaluation of toxic effect of phenanthrene exposure to zebrafish by transcriptional approaches. Our findings could present foundation for further study on molecular mechanism responsible for zebrafish's responses to phenanthrene exposure.", null, null, "Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L  and livers were sampled and pooled", null, "PHE15d.1", null, "strain:not applicable|isolate:not applicable|breed:AB line|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:Adult fish|sex:pooled male and female|tissue:liver|biomaterial provider:China Zebrafish Resource Center|birth location:Wuhan  China|breeding method:maintained in the semi static system under conditions of water quality and illumination as follows: temperature 2327   pH 78  dissolved oxygen concentration 5 mg   L 1  total hardness 10250 mg CaCO3 per liter  and light/dark period of 12:12 h.|genotype:AB line|health state:Healthy|sample type:tissue sample|treatment:Fish exposed to phenanthrene for xxx day at concentration of 300 g L 1|replicate:biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day", "PHE15d.1", "PHE15d.1", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP136856", null, null, "PHE15d_1_1.fq.gz PHE15d_1_2.fq.gz", "fastq fastq", 8022302100.0, 26741007.0, "PHE15d 1 1.fq.gz", "0:150 1:150", "A:2050760820;C:1951106961;G:1960909235;T:2054339788;N:5185296", 150, 150, null, null, 2050760820, 1951106961, 1960909235, 2054339788, 5185296, "SRX3869065", "SRS3112040", "SRA678027", "Pearl River Fisheries Research Institute, CAFS|Fisheries environmental protection laboratory", "Pearl River Fisheries Research Institute, CAFS", 2, 0.93832, 0.94188, 0.03193, 0.03228, 0.77828, 0.78632, 0.5109, 0.50873, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-03-31", "Adult", "Adult", "Liver", "Liver and Biliary System"], [48046, "SRR6921828", "SRX3869064", "SRS3112039", "SRP136856", "PRJNA448207", "Transcriptomic profiles of zebrafish liver exposed to phenanthrene", "PRJNA448207", "Other", "The present study aims to examine the toxicological effects of phenanthrene in the molecular mechanism in zebrafish. We performed RNA Seq analysis on zebrafish liver responding to phenanthrene exposure. Genes involved in phenanthrene exposure to zebrafish liver were identified from the transcriptional data. This study provides the completed evaluation of toxic effect of phenanthrene exposure to zebrafish by transcriptional approaches. Our findings could present foundation for further study on molecular mechanism responsible for zebrafish's responses to phenanthrene exposure.", null, null, "Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L  and livers were sampled and pooled", null, "PHE15d.2", null, "strain:not applicable|isolate:not applicable|breed:AB line|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:Adult fish|sex:pooled male and female|tissue:liver|biomaterial provider:China Zebrafish Resource Center|birth location:Wuhan  China|breeding method:maintained in the semi static system under conditions of water quality and illumination as follows: temperature 2327   pH 78  dissolved oxygen concentration 5 mg   L 1  total hardness 10250 mg CaCO3 per liter  and light/dark period of 12:12 h.|genotype:AB line|health state:Healthy|sample type:tissue sample|treatment:Fish exposed to phenanthrene for xxx day at concentration of 300 g L 1|replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day", "PHE15d.2", "PHE15d.2", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP136856", null, null, "PHE15d_2_1.fq.gz PHE15d_2_2.fq.gz", "fastq fastq", 8034285000.0, 26780950.0, "PHE15d 2 2.fq.gz", "0:150 1:150", "A:2073938434;C:1941404499;G:1938205281;T:2075525314;N:5211472", 150, 150, null, null, 2073938434, 1941404499, 1938205281, 2075525314, 5211472, "SRX3869064", "SRS3112039", "SRA678027", "Pearl River Fisheries Research Institute, CAFS|Fisheries environmental protection laboratory", "Pearl River Fisheries Research Institute, CAFS", 2, 0.93687, 0.93932, 0.0343, 0.03469, 0.74797, 0.75676, 0.46939, 0.48083, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-03-31", "Adult", "Adult", "Liver", "Liver and Biliary System"], [48047, "SRR6921829", "SRX3869063", "SRS3112038", "SRP136856", "PRJNA448207", "Transcriptomic profiles of zebrafish liver exposed to phenanthrene", "PRJNA448207", "Other", "The present study aims to examine the toxicological effects of phenanthrene in the molecular mechanism in zebrafish. We performed RNA Seq analysis on zebrafish liver responding to phenanthrene exposure. Genes involved in phenanthrene exposure to zebrafish liver were identified from the transcriptional data. This study provides the completed evaluation of toxic effect of phenanthrene exposure to zebrafish by transcriptional approaches. Our findings could present foundation for further study on molecular mechanism responsible for zebrafish's responses to phenanthrene exposure.", null, null, "Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L  and livers were sampled and pooled", null, "PHE15d.3", null, "strain:not applicable|isolate:not applicable|breed:AB line|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:Adult fish|sex:pooled male and female|tissue:liver|biomaterial provider:China Zebrafish Resource Center|birth location:Wuhan  China|breeding method:maintained in the semi static system under conditions of water quality and illumination as follows: temperature 2327   pH 78  dissolved oxygen concentration 5 mg   L 1  total hardness 10250 mg CaCO3 per liter  and light/dark period of 12:12 h.|genotype:AB line|health state:Healthy|sample type:tissue sample|treatment:Fish exposed to phenanthrene for xxx day at concentration of 300 g L 1|replicate:biological replicate 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"PRJNA543743", "Whole Genome Sequencing", "Zebrafish is increasingly being used to study liver injury and regeneration. However  very little is known about molecular players that respond to injury and those important for liver regeneration. We use a metronidazole nitroreductase MTZ nfsb based system to selectively ablate hepatocytes in adult zebrafish to create a model for liver injury and regeneration. Here  we generate a comprehensive temporal map of gene expression changes during regeneration through RNA sequencing of liver samples at various stages of injury and regeneration. Analysing this data  we find that xxx post injury the immediate early transcription factor MYC induces a battery of genes that respond to the metronidazole induced ROS by activating oxido reductase pathways and apoptosis machinery. xxx post injury  liver cells down regulate many functional genes including complement protein synthesis  bile acid and lipid biosynthesis  in a concerted manner. At 6 xxx post injury  we find a dramatic induction of cholesterol biosynthesis and protein folding machinery  with expression levels returning to pre damage levels by 8 days  suggesting an important role for these pathways in liver regeneration. This chronological transcriptomic map of liver regeneration in zebrafish would serve as a framework for further studies in understanding  and for screening for compounds that augment liver regeneration.", null, null, null, null, "t3", null, "strain:Transgenic|age:1year|dev stage:adult|sex:female|tissue:liver|disease stg:0hpd|Replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "t3 rep2", "t3 rep2", "t3 rep2", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP199854", null, null, "0hpd_Rep2_R1.fastq.gz 0hpd_Rep2_R2.fastq.gz", "fastq fastq", 21952466700.0, 73174889.0, "0hpd Rep2 R1.fastq.gz", "0:150 1:150", "A:5618990934;C:5293215751;G:5219181872;T:5818536076;N:2542067", 150, 150, null, null, 5618990934, 5293215751, 5219181872, 5818536076, 2542067, "SRX5933020", "SRS4846227", "SRA891455", "CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.96228, 0.94387, 0.07627, 0.07055, 0.89051, 0.89485, 0.13962, 0.13552, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2019-05-30", "Adult", "Adult", "Liver", "Liver and Biliary System"], [52297, "SRR9159930", "SRX5933019", "SRS4846226", "SRP199854", "PRJNA543743", "A temporal map of gene expression pattern during zebrafish liver regeneration.", "PRJNA543743", "Whole Genome Sequencing", "Zebrafish is increasingly being used to study liver injury and regeneration. However  very little is known about molecular players that respond to injury and those important for liver regeneration. We use a metronidazole nitroreductase MTZ nfsb based system to selectively ablate hepatocytes in adult zebrafish to create a model for liver injury and regeneration. Here  we generate a comprehensive temporal map of gene expression changes during regeneration through RNA sequencing of liver samples at various stages of injury and regeneration. Analysing this data  we find that xxx post injury the immediate early transcription factor MYC induces a battery of genes that respond to the metronidazole induced ROS by activating oxido reductase pathways and apoptosis machinery. xxx post injury  liver cells down regulate many functional genes including complement protein synthesis  bile acid and lipid biosynthesis  in a concerted manner. At 6 xxx post injury  we find a dramatic induction of cholesterol biosynthesis and protein folding machinery  with expression levels returning to pre damage levels by 8 days  suggesting an important role for these pathways in liver regeneration. This chronological transcriptomic map of liver regeneration in zebrafish would serve as a framework for further studies in understanding  and for screening for compounds that augment liver regeneration.", null, null, null, null, "t3 rep1", null, "strain:Transgenic|age:1year|dev stage:adult|sex:female|tissue:liver|disease stg:0hpd|Replicate:biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "t3 rep1", "t3 rep1", "t3 rep1", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP199854", null, null, "0hpd_Rep1_R1.fastq.gz 0hpd_Rep1_R2.fastq.gz", "fastq fastq", 15401555400.0, 55005555.0, "0hpd Rep1 R1.fastq.gz", "0:140 1:140", "A:3872870367;C:3823452006;G:3663205853;T:3999933116;N:42094058", 140, 140, null, null, 3872870367, 3823452006, 3663205853, 3999933116, 42094058, "SRX5933019", "SRS4846226", "SRA891455", "CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.95255, 0.84305, 0.08499, 0.07143, 0.90313, 0.9106, 0.16838, 0.14433, 140, 140, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2019-05-30", "Adult", "Adult", "Liver", "Liver and Biliary System"], [52298, "SRR9159931", "SRX5933018", "SRS4846225", "SRP199854", "PRJNA543743", "A temporal map of gene expression pattern during zebrafish liver regeneration.", "PRJNA543743", "Whole Genome Sequencing", "Zebrafish is increasingly being used to study liver injury and regeneration. However  very little is known about molecular players that respond to injury and those important for liver regeneration. We use a metronidazole nitroreductase MTZ nfsb based system to selectively ablate hepatocytes in adult zebrafish to create a model for liver injury and regeneration. Here  we generate a comprehensive temporal map of gene expression changes during regeneration through RNA sequencing of liver samples at various stages of injury and regeneration. Analysing this data  we find that xxx post injury the immediate early transcription factor MYC induces a battery of genes that respond to the metronidazole induced ROS by activating oxido reductase pathways and apoptosis machinery. xxx post injury  liver cells down regulate many functional genes including complement protein synthesis  bile acid and lipid biosynthesis  in a concerted manner. At 6 xxx post injury  we find a dramatic induction of cholesterol biosynthesis and protein folding machinery  with expression levels returning to pre damage levels by 8 days  suggesting an important role for these pathways in liver regeneration. This chronological transcriptomic map of liver regeneration in zebrafish would serve as a framework for further studies in understanding  and for screening for compounds that augment liver regeneration.", null, null, null, null, "t0", null, "strain:Transgenic|age:1year|dev stage:adult|sex:female|tissue:liver|disease stg:untreated|Replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "t0 rep2", "t0 rep2", "t0 rep2", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP199854", null, null, "Untreated_Rep2_R1.fastq.gz Untreated_Rep2_R2.fastq.gz", "fastq fastq", 11691778800.0, 38972596.0, "Untreated Rep2 R1.fastq.gz", "0:150 1:150", "A:3033793988;C:2830158145;G:2751857668;T:3074605384;N:1363615", 150, 150, null, null, 3033793988, 2830158145, 2751857668, 3074605384, 1363615, "SRX5933018", "SRS4846225", "SRA891455", "CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.95558, 0.93747, 0.10942, 0.10027, 0.852, 0.85967, 0.25273, 0.25263, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2019-05-30", "Adult", "Adult", "Liver", "Liver and Biliary System"], [52299, "SRR9159932", "SRX5933017", "SRS4846224", "SRP199854", "PRJNA543743", "A temporal map of gene expression pattern during zebrafish liver regeneration.", "PRJNA543743", "Whole Genome Sequencing", "Zebrafish is increasingly being used to study liver injury and regeneration. However  very little is known about molecular players that respond to injury and those important for liver regeneration. We use a metronidazole nitroreductase MTZ nfsb based system to selectively ablate hepatocytes in adult zebrafish to create a model for liver injury and regeneration. Here  we generate a comprehensive temporal map of gene expression changes during regeneration through RNA sequencing of liver samples at various stages of injury and regeneration. Analysing this data  we find that xxx post injury the immediate early transcription factor MYC induces a battery of genes that respond to the metronidazole induced ROS by activating oxido reductase pathways and apoptosis machinery. xxx post injury  liver cells down regulate many functional genes including complement protein synthesis  bile acid and lipid biosynthesis  in a concerted manner. At 6 xxx post injury  we find a dramatic induction of cholesterol biosynthesis and protein folding machinery  with expression levels returning to pre damage levels by 8 days  suggesting an important role for these pathways in liver regeneration. This chronological transcriptomic map of liver regeneration in zebrafish would serve as a framework for further studies in understanding  and for screening for compounds that augment liver regeneration.", null, null, null, null, "t0 rep1", null, "strain:Transgenic|age:1year|dev stage:adult|sex:female|tissue:liver|disease stg:untreated|Replicate:biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "t0 rep1", "t0 rep1", "t0 rep1", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP199854", null, null, "Untreated_Rep1_R1.fastq.gz Untreated_Rep1_R2.fastq.gz", "fastq fastq", 15183490000.0, 54226750.0, "Untreated Rep1 R1.fastq.gz", "0:140 1:140", "A:3868549452;C:3725214028;G:3555537015;T:3992531756;N:41657749", 140, 140, null, null, 3868549452, 3725214028, 3555537015, 3992531756, 41657749, "SRX5933017", "SRS4846224", "SRA891455", "CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.92869, 0.82319, 0.15668, 0.1344, 0.80052, 0.81067, 0.44034, 0.43611, 140, 140, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2019-05-30", "Adult", "Adult", "Liver", "Liver and Biliary System"], [52300, "SRR9159933", "SRX5933016", "SRS4846223", "SRP199854", "PRJNA543743", "A temporal map of gene expression pattern during zebrafish liver regeneration.", "PRJNA543743", "Whole Genome Sequencing", "Zebrafish is increasingly being used to study liver injury and regeneration. However  very little is known about molecular players that respond to injury and those important for liver regeneration. We use a metronidazole nitroreductase MTZ nfsb based system to selectively ablate hepatocytes in adult zebrafish to create a model for liver injury and regeneration. Here  we generate a comprehensive temporal map of gene expression changes during regeneration through RNA sequencing of liver samples at various stages of injury and regeneration. Analysing this data  we find that xxx post injury the immediate early transcription factor MYC induces a battery of genes that respond to the metronidazole induced ROS by activating oxido reductase pathways and apoptosis machinery. xxx post injury  liver cells down regulate many functional genes including complement protein synthesis  bile acid and lipid biosynthesis  in a concerted manner. At 6 xxx post injury  we find a dramatic induction of cholesterol biosynthesis and protein folding machinery  with expression levels returning to pre damage levels by 8 days  suggesting an important role for these pathways in liver regeneration. This chronological transcriptomic map of liver regeneration in zebrafish would serve as a framework for further studies in understanding  and for screening for compounds that augment liver regeneration.", null, null, null, null, "t27", null, "strain:Transgenic|age:1year|dev stage:adult|sex:female|tissue:liver|disease stg:24hpd|Replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "t27 rep2", "t27 rep2", "t27 rep2", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP199854", null, null, "24hpd_Rep2_R1.fastq.gz 24hpd_Rep2_R2.fastq.gz", "fastq fastq", 11418804900.0, 38062683.0, "24hpd Rep2 R1.fastq.gz", "0:150 1:150", "A:2757590450;C:2919048251;G:2847621742;T:2877591783;N:16952674", 150, 150, null, null, 2757590450, 2919048251, 2847621742, 2877591783, 16952674, "SRX5933016", "SRS4846223", "SRA891455", "CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.79128, 0.76005, 0.11901, 0.10864, 0.85713, 0.8565, 0.30968, 0.29689, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2019-05-30", "Adult", "Adult", "Liver", "Liver and Biliary System"], [52301, "SRR9159934", "SRX5933015", "SRS4846222", "SRP199854", "PRJNA543743", "A temporal map of gene expression pattern during zebrafish liver regeneration.", "PRJNA543743", "Whole Genome Sequencing", "Zebrafish is increasingly being used to study liver injury and regeneration. However  very little is known about molecular players that respond to injury and those important for liver regeneration. We use a metronidazole nitroreductase MTZ nfsb based system to selectively ablate hepatocytes in adult zebrafish to create a model for liver injury and regeneration. Here  we generate a comprehensive temporal map of gene expression changes during regeneration through RNA sequencing of liver samples at various stages of injury and regeneration. Analysing this data  we find that xxx post injury the immediate early transcription factor MYC induces a battery of genes that respond to the metronidazole induced ROS by activating oxido reductase pathways and apoptosis machinery. xxx post injury  liver cells down regulate many functional genes including complement protein synthesis  bile acid and lipid biosynthesis  in a concerted manner. At 6 xxx post injury  we find a dramatic induction of cholesterol biosynthesis and protein folding machinery  with expression levels returning to pre damage levels by 8 days  suggesting an important role for these pathways in liver regeneration. This chronological transcriptomic map of liver regeneration in zebrafish would serve as a framework for further studies in understanding  and for screening for compounds that augment liver regeneration.", null, null, null, null, "t27 rep1", null, "strain:Transgenic|age:1year|dev stage:adult|sex:female|tissue:liver|disease stg:24hpd|Replicate:biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "t27 rep1", "t27 rep1", "t27 rep1", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP199854", null, null, "24hpd_Rep1_R1.fastq.gz 24hpd_Rep1_R2.fastq.gz", "fastq fastq", 11562586280.0, 41294951.0, "24hpd Rep1 R1.fastq.gz", "0:140 1:140", "A:2905792843;C:2878687498;G:2769983219;T:2976280146;N:31842574", 140, 140, null, null, 2905792843, 2878687498, 2769983219, 2976280146, 31842574, "SRX5933015", "SRS4846222", "SRA891455", "CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.92725, 0.81984, 0.15675, 0.13356, 0.83163, 0.84129, 0.30774, 0.29041, 140, 140, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2019-05-30", "Adult", "Adult", "Liver", "Liver and Biliary System"], [52302, "SRR9159935", "SRX5933014", "SRS4846221", "SRP199854", "PRJNA543743", "A temporal map of gene expression pattern during zebrafish liver regeneration.", "PRJNA543743", "Whole Genome Sequencing", "Zebrafish is increasingly being used to study liver injury and regeneration. However  very little is known about molecular players that respond to injury and those important for liver regeneration. We use a metronidazole nitroreductase MTZ nfsb based system to selectively ablate hepatocytes in adult zebrafish to create a model for liver injury and regeneration. Here  we generate a comprehensive temporal map of gene expression changes during regeneration through RNA sequencing of liver samples at various stages of injury and regeneration. Analysing this data  we find that xxx post injury the immediate early transcription factor MYC induces a battery of genes that respond to the metronidazole induced ROS by activating oxido reductase pathways and apoptosis machinery. xxx post injury  liver cells down regulate many functional genes including complement protein synthesis  bile acid and lipid biosynthesis  in a concerted manner. At 6 xxx post injury  we find a dramatic induction of cholesterol biosynthesis and protein folding machinery  with expression levels returning to pre damage levels by 8 days  suggesting an important role for these pathways in liver regeneration. This chronological transcriptomic map of liver regeneration in zebrafish would serve as a framework for further studies in understanding  and for screening for compounds that augment liver regeneration.", null, null, null, null, "t15", null, "strain:Transgenic|age:1year|dev stage:adult|sex:female|tissue:liver|disease stg:12hpd|Replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "t15 rep2", "t15 rep2", "t15 rep2", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP199854", null, null, "12hpd_Rep2_R1.fastq.gz 12hpd_Rep2_R2.fastq.gz", "fastq fastq", 15115234800.0, 50384116.0, "12hpd Rep2 R1.fastq.gz", "0:150 1:150", "A:3908350165;C:3644488292;G:3666423006;T:3873518947;N:22454390", 150, 150, null, null, 3908350165, 3644488292, 3666423006, 3873518947, 22454390, "SRX5933014", "SRS4846221", "SRA891455", "CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.944, 0.92096, 0.1208, 0.11295, 0.81947, 0.82171, 0.21089, 0.20764, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2019-05-30", "Adult", "Adult", "Liver", "Liver and Biliary System"], [52303, "SRR9159936", "SRX5933013", "SRS4846220", "SRP199854", "PRJNA543743", "A temporal map of gene expression pattern during zebrafish liver regeneration.", "PRJNA543743", "Whole Genome Sequencing", "Zebrafish is increasingly being used to study liver injury and regeneration. However  very little is known about molecular players that respond to injury and those important for liver regeneration. We use a metronidazole nitroreductase MTZ nfsb based system to selectively ablate hepatocytes in adult zebrafish to create a model for liver injury and regeneration. Here  we generate a comprehensive temporal map of gene expression changes during regeneration through RNA sequencing of liver samples at various stages of injury and regeneration. Analysing this data  we find that xxx post injury the immediate early transcription factor MYC induces a battery of genes that respond to the metronidazole induced ROS by activating oxido reductase pathways and apoptosis machinery. xxx post injury  liver cells down regulate many functional genes including complement protein synthesis  bile acid and lipid biosynthesis  in a concerted manner. At 6 xxx post injury  we find a dramatic induction of cholesterol biosynthesis and protein folding machinery  with expression levels returning to pre damage levels by 8 days  suggesting an important role for these pathways in liver regeneration. This chronological transcriptomic map of liver regeneration in zebrafish would serve as a framework for further studies in understanding  and for screening for compounds that augment liver regeneration.", null, null, null, null, "t15 rep1", null, "strain:Transgenic|age:1year|dev stage:adult|sex:female|tissue:liver|disease stg:12hpd|Replicate:biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "t15 rep1", "t15 rep1", "t15 rep1", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP199854", null, null, "12hpd_Rep1_R1.fastq.gz 12hpd_Rep1_R2.fastq.gz", "fastq fastq", 12810625800.0, 45752235.0, "12hpd Rep1 R1.fastq.gz", "0:140 1:140", "A:3255395442;C:3139425049;G:3017948274;T:3362649088;N:35207947", 140, 140, null, null, 3255395442, 3139425049, 3017948274, 3362649088, 35207947, "SRX5933013", "SRS4846220", "SRA891455", "CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.93088, 0.82263, 0.10483, 0.08867, 0.84928, 0.85713, 0.20633, 0.201, 140, 140, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2019-05-30", "Adult", "Adult", "Liver", "Liver and Biliary System"], [52304, "SRR9159937", "SRX5933012", "SRS4846219", "SRP199854", "PRJNA543743", "A temporal map of gene expression pattern during zebrafish liver regeneration.", "PRJNA543743", "Whole Genome Sequencing", "Zebrafish is increasingly being used to study liver injury and regeneration. However  very little is known about molecular players that respond to injury and those important for liver regeneration. We use a metronidazole nitroreductase MTZ nfsb based system to selectively ablate hepatocytes in adult zebrafish to create a model for liver injury and regeneration. Here  we generate a comprehensive temporal map of gene expression changes during regeneration through RNA sequencing of liver samples at various stages of injury and regeneration. Analysing this data  we find that xxx post injury the immediate early transcription factor MYC induces a battery of genes that respond to the metronidazole induced ROS by activating oxido reductase pathways and apoptosis machinery. xxx post injury  liver cells down regulate many functional genes including complement protein synthesis  bile acid and lipid biosynthesis  in a concerted manner. At 6 xxx post injury  we find a dramatic induction of cholesterol biosynthesis and protein folding machinery  with expression levels returning to pre damage levels by 8 days  suggesting an important role for these pathways in liver regeneration. This chronological transcriptomic map of liver regeneration in zebrafish would serve as a framework for further studies in understanding  and for screening for compounds that augment liver regeneration.", null, null, null, null, "t99", null, "strain:Transgenic|age:1year|dev stage:adult|sex:female|tissue:liver|disease stg:4dpd|Replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "t99 rep2", "t99 rep2", "t99 rep2", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP199854", null, null, "4dpd_Rep2_R1.fastq.gz 4dpd_Rep2_R2.fastq.gz", "fastq fastq", 11147062500.0, 37156875.0, "4dpd Rep2 R1.fastq.gz", "0:150 1:150", "A:2868182525;C:2710375516;G:2681887164;T:2870023400;N:16593895", 150, 150, null, null, 2868182525, 2710375516, 2681887164, 2870023400, 16593895, "SRX5933012", "SRS4846219", "SRA891455", "CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.91761, 0.8937, 0.13281, 0.12573, 0.84177, 0.84547, 0.20435, 0.20185, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2019-05-30", "Adult", "Adult", "Liver", "Liver and Biliary System"], [52305, "SRR9159938", "SRX5933011", "SRS4846218", "SRP199854", "PRJNA543743", "A temporal map of gene expression pattern during zebrafish liver regeneration.", "PRJNA543743", "Whole Genome Sequencing", "Zebrafish is increasingly being used to study liver injury and regeneration. However  very little is known about molecular players that respond to injury and those important for liver regeneration. We use a metronidazole nitroreductase MTZ nfsb based system to selectively ablate hepatocytes in adult zebrafish to create a model for liver injury and regeneration. Here  we generate a comprehensive temporal map of gene expression changes during regeneration through RNA sequencing of liver samples at various stages of injury and regeneration. Analysing this data  we find that xxx post injury the immediate early transcription factor MYC induces a battery of genes that respond to the metronidazole induced ROS by activating oxido reductase pathways and apoptosis machinery. xxx post injury  liver cells down regulate many functional genes including complement protein synthesis  bile acid and lipid biosynthesis  in a concerted manner. At 6 xxx post injury  we find a dramatic induction of cholesterol biosynthesis and protein folding machinery  with expression levels returning to pre damage levels by 8 days  suggesting an important role for these pathways in liver regeneration. This chronological transcriptomic map of liver regeneration in zebrafish would serve as a framework for further studies in understanding  and for screening for compounds that augment liver regeneration.", null, null, null, null, "t99 rep1", null, "strain:Transgenic|age:1year|dev stage:adult|sex:female|tissue:liver|disease stg:4dpd|Replicate:biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "t99 rep1", "t99 rep1", "t99 rep1", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP199854", null, null, "4dpd_Rep1_R1.fastq.gz 4dpd_Rep1_R2.fastq.gz", "fastq fastq", 16598672160.0, 59280972.0, "4dpd Rep1 R1.fastq.gz", "0:140 1:140", "A:4283950233;C:4093317814;G:3949933855;T:4270009528;N:1460730", 140, 140, null, null, 4283950233, 4093317814, 3949933855, 4270009528, 1460730, "SRX5933011", "SRS4846218", "SRA891455", "CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.94341, 0.92503, 0.1066, 0.0991, 0.87326, 0.87229, 0.16235, 0.15969, 140, 140, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2019-05-30", "Adult", "Adult", "Liver", "Liver and Biliary System"], [52306, "SRR9159939", "SRX5933010", "SRS4846217", "SRP199854", "PRJNA543743", "A temporal map of gene expression pattern during zebrafish liver regeneration.", "PRJNA543743", "Whole Genome Sequencing", "Zebrafish is increasingly being used to study liver injury and regeneration. However  very little is known about molecular players that respond to injury and those important for liver regeneration. We use a metronidazole nitroreductase MTZ nfsb based system to selectively ablate hepatocytes in adult zebrafish to create a model for liver injury and regeneration. Here  we generate a comprehensive temporal map of gene expression changes during regeneration through RNA sequencing of liver samples at various stages of injury and regeneration. Analysing this data  we find that xxx post injury the immediate early transcription factor MYC induces a battery of genes that respond to the metronidazole induced ROS by activating oxido reductase pathways and apoptosis machinery. xxx post injury  liver cells down regulate many functional genes including complement protein synthesis  bile acid and lipid biosynthesis  in a concerted manner. At 6 xxx post injury  we find a dramatic induction of cholesterol biosynthesis and protein folding machinery  with expression levels returning to pre damage levels by 8 days  suggesting an important role for these pathways in liver regeneration. This chronological transcriptomic map of liver regeneration in zebrafish would serve as a framework for further studies in understanding  and for screening for compounds that augment liver regeneration.", null, null, null, null, "t147", null, "strain:Transgenic|age:1year|dev stage:adult|sex:female|tissue:liver|disease stg:6dpd|Replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "t147 rep2", "t147 rep2", "t147 rep2", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP199854", null, null, "6dpd_Rep2_R1.fastq.gz 6dpd_Rep2_R2.fastq.gz", "fastq fastq", 15662541600.0, 52208472.0, "6dpd Rep2 R1.fastq.gz", "0:150 1:150", "A:4066415508;C:3751047766;G:3666463352;T:4108015506;N:70599468", 150, 150, null, null, 4066415508, 3751047766, 3666463352, 4108015506, 70599468, "SRX5933010", "SRS4846217", "SRA891455", "CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.96838, 0.73281, 0.08125, 0.05335, 0.90439, 0.92941, 0.11546, 0.11533, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2019-05-30", "Adult", "Adult", "Liver", "Liver and Biliary System"], [52307, "SRR9159940", "SRX5933009", "SRS4846216", "SRP199854", "PRJNA543743", "A temporal map of gene expression pattern during zebrafish liver regeneration.", "PRJNA543743", "Whole Genome Sequencing", "Zebrafish is increasingly being used to study liver injury and regeneration. However  very little is known about molecular players that respond to injury and those important for liver regeneration. We use a metronidazole nitroreductase MTZ nfsb based system to selectively ablate hepatocytes in adult zebrafish to create a model for liver injury and regeneration. Here  we generate a comprehensive temporal map of gene expression changes during regeneration through RNA sequencing of liver samples at various stages of injury and regeneration. Analysing this data  we find that xxx post injury the immediate early transcription factor MYC induces a battery of genes that respond to the metronidazole induced ROS by activating oxido reductase pathways and apoptosis machinery. xxx post injury  liver cells down regulate many functional genes including complement protein synthesis  bile acid and lipid biosynthesis  in a concerted manner. At 6 xxx post injury  we find a dramatic induction of cholesterol biosynthesis and protein folding machinery  with expression levels returning to pre damage levels by 8 days  suggesting an important role for these pathways in liver regeneration. This chronological transcriptomic map of liver regeneration in zebrafish would serve as a framework for further studies in understanding  and for screening for compounds that augment liver regeneration.", null, null, null, null, "t147 rep1", null, "strain:Transgenic|age:1year|dev stage:adult|sex:female|tissue:liver|disease stg:6dpd|Replicate:biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "t147 rep1", "t147 rep1", "t147 rep1", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP199854", null, null, "6dpd_Rep1_R1.fastq.gz 6dpd_Rep1_R2.fastq.gz", "fastq fastq", 16001623120.0, 57148654.0, "6dpd Rep1 R1.fastq.gz", "0:140 1:140", "A:4068927256;C:4021429619;G:3843587165;T:4066289010;N:1390070", 140, 140, null, null, 4068927256, 4021429619, 3843587165, 4066289010, 1390070, "SRX5933009", "SRS4846216", "SRA891455", "CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.94429, 0.9233, 0.08138, 0.07568, 0.89203, 0.88846, 0.17226, 0.1635, 140, 140, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2019-05-30", "Adult", "Adult", "Liver", "Liver and Biliary System"], [52308, "SRR9159941", "SRX5933008", "SRS4846215", "SRP199854", "PRJNA543743", "A temporal map of gene expression pattern during zebrafish liver regeneration.", "PRJNA543743", "Whole Genome Sequencing", "Zebrafish is increasingly being used to study liver injury and regeneration. However  very little is known about molecular players that respond to injury and those important for liver regeneration. We use a metronidazole nitroreductase MTZ nfsb based system to selectively ablate hepatocytes in adult zebrafish to create a model for liver injury and regeneration. Here  we generate a comprehensive temporal map of gene expression changes during regeneration through RNA sequencing of liver samples at various stages of injury and regeneration. Analysing this data  we find that xxx post injury the immediate early transcription factor MYC induces a battery of genes that respond to the metronidazole induced ROS by activating oxido reductase pathways and apoptosis machinery. xxx post injury  liver cells down regulate many functional genes including complement protein synthesis  bile acid and lipid biosynthesis  in a concerted manner. At 6 xxx post injury  we find a dramatic induction of cholesterol biosynthesis and protein folding machinery  with expression levels returning to pre damage levels by 8 days  suggesting an important role for these pathways in liver regeneration. This chronological transcriptomic map of liver regeneration in zebrafish would serve as a framework for further studies in understanding  and for screening for compounds that augment liver regeneration.", null, null, null, null, "t195", null, "strain:Transgenic|age:1year|dev stage:adult|sex:female|tissue:liver|disease stg:8dpd|Replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "t195 rep2", "t195 rep2", "t195 rep2", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP199854", null, null, "8dpd_Rep2_R1.fastq.gz 8dpd_Rep2_R2.fastq.gz", "fastq fastq", 5858110500.0, 19527035.0, "8dpd Rep2 R1.fastq.gz", "0:150 1:150", "A:1537845807;C:1386461476;G:1372735432;T:1533504707;N:27563078", 150, 150, null, null, 1537845807, 1386461476, 1372735432, 1533504707, 27563078, "SRX5933008", "SRS4846215", "SRA891455", "CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.95004, 0.67359, 0.11276, 0.0681, 0.86085, 0.90901, 0.18762, 0.18351, 150, 150, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2019-05-30", "Adult", "Adult", "Liver", "Liver and Biliary System"], [52309, "SRR9159942", "SRX5933007", "SRS4846214", "SRP199854", "PRJNA543743", "A temporal map of gene expression pattern during zebrafish liver regeneration.", "PRJNA543743", "Whole Genome Sequencing", "Zebrafish is increasingly being used to study liver injury and regeneration. However  very little is known about molecular players that respond to injury and those important for liver regeneration. We use a metronidazole nitroreductase MTZ nfsb based system to selectively ablate hepatocytes in adult zebrafish to create a model for liver injury and regeneration. Here  we generate a comprehensive temporal map of gene expression changes during regeneration through RNA sequencing of liver samples at various stages of injury and regeneration. Analysing this data  we find that xxx post injury the immediate early transcription factor MYC induces a battery of genes that respond to the metronidazole induced ROS by activating oxido reductase pathways and apoptosis machinery. xxx post injury  liver cells down regulate many functional genes including complement protein synthesis  bile acid and lipid biosynthesis  in a concerted manner. At 6 xxx post injury  we find a dramatic induction of cholesterol biosynthesis and protein folding machinery  with expression levels returning to pre damage levels by 8 days  suggesting an important role for these pathways in liver regeneration. This chronological transcriptomic map of liver regeneration in zebrafish would serve as a framework for further studies in understanding  and for screening for compounds that augment liver regeneration.", null, null, null, null, "t195 rep1", null, "strain:Transgenic|age:1year|dev stage:adult|sex:female|tissue:liver|disease stg:8dpd|Replicate:biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "t195 rep1", "t195 rep1", "t195 rep1", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP199854", null, null, "8dpd_Rep1_R1.fastq.gz 8dpd_Rep1_R2.fastq.gz", "fastq fastq", 15843284800.0, 56583160.0, "8dpd Rep1 R1.fastq.gz", "0:140 1:140", "A:4004856999;C:3934342452;G:3949119168;T:3946497372;N:8468809", 140, 140, null, null, 4004856999, 3934342452, 3949119168, 3946497372, 8468809, "SRX5933007", "SRS4846214", "SRA891455", "CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.89714, 0.87074, 0.09745, 0.09052, 0.86482, 0.86342, 0.20854, 0.20127, 140, 140, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2019-05-30", "Adult", "Adult", "Liver", "Liver and Biliary System"], [52344, "SRR9182350", "SRX5954864", "SRS4865355", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain NAC.ACR NV 22", "NV 22", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:N acetyl L cysteine \u2013 Acrylamide replicate 6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: NAC ACR treatment adult male brain", "NV 22", "NV 22", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-22-TTACGTGC-AGACCTTG_S370_R1_001.fastq.gz 2465-NV-22-TTACGTGC-AGACCTTG_S370_R2_001.fastq.gz", "fastq fastq", 11819786100.0, 39399287.0, "2465 NV 22 TTACGTGC AGACCTTG S370 R1 001.fastq.gz", "0:150 1:150", "A:3380503046;C:2495962964;G:2656047304;T:3270872050;N:16400736", 150, 150, null, null, 3380503046, 2495962964, 2656047304, 3270872050, 16400736, "SRX5954864", "SRS4865355", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.91494, 0.91128, 0.18909, 0.18574, 0.71108, 0.71137, 0.48868, 0.499, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52345, "SRR9182351", "SRX5954863", "SRS4865356", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain NAC.ACR NV 21", "NV 21", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:N acetyl L cysteine \u2013 Acrylamide replicate 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: NAC ACR treatment adult male brain", "NV 21", "NV 21", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-21-CACAGACT-CTGTACCA_S369_R1_001.fastq.gz 2465-NV-21-CACAGACT-CTGTACCA_S369_R2_001.fastq.gz", "fastq fastq", 10663919700.0, 35546399.0, "2465 NV 21 CACAGACT CTGTACCA S369 R1 001.fastq.gz", "0:150 1:150", "A:3044142401;C:2256718117;G:2404580970;T:2943582444;N:14895768", 150, 150, null, null, 3044142401, 2256718117, 2404580970, 2943582444, 14895768, "SRX5954863", "SRS4865356", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.91165, 0.91549, 0.18677, 0.18546, 0.71127, 0.71112, 0.49855, 0.50317, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52346, "SRR9182352", "SRX5954862", "SRS4865354", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain NAC.ACR NV 24", "NV 24", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:N acetyl L cysteine \u2013 Acrylamide replicate 8|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: NAC ACR treatment adult male brain", "NV 24", "NV 24", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-24-CACGCAAT-CCTTCCAT_S372_R1_001.fastq.gz 2465-NV-24-CACGCAAT-CCTTCCAT_S372_R2_001.fastq.gz", "fastq fastq", 13721223900.0, 45737413.0, "2465 NV 24 CACGCAAT CCTTCCAT S372 R1 001.fastq.gz", "0:150 1:150", "A:3890225027;C:2875058260;G:3195515732;T:3741344065;N:19080816", 150, 150, null, null, 3890225027, 2875058260, 3195515732, 3741344065, 19080816, "SRX5954862", "SRS4865354", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.90192, 0.90137, 0.19497, 0.19179, 0.7138, 0.71141, 0.49776, 0.4936, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52347, "SRR9182353", "SRX5954861", "SRS4865353", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain NAC.ACR NV 23", "NV 23", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:N acetyl L cysteine \u2013 Acrylamide replicate 7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: NAC ACR treatment adult male brain", "NV 23", "NV 23", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-23-CCAAGGTT-AGGATAGC_S371_R1_001.fastq.gz 2465-NV-23-CCAAGGTT-AGGATAGC_S371_R2_001.fastq.gz", "fastq fastq", 14683576200.0, 48945254.0, "2465 NV 23 CCAAGGTT AGGATAGC S371 R1 001.fastq.gz", "0:150 1:150", "A:4153451869;C:3142795551;G:3335897512;T:4030892485;N:20538783", 150, 150, null, null, 4153451869, 3142795551, 3335897512, 4030892485, 20538783, "SRX5954861", "SRS4865353", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.91115, 0.91565, 0.18214, 0.18219, 0.70804, 0.70676, 0.49259, 0.50002, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52348, "SRR9182354", "SRX5954860", "SRS4865352", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain NAC.ACR NV 19", "NV 19", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:N acetyl L cysteine \u2013 Acrylamide replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: NAC ACR treatment adult male brain", "NV 19", "NV 19", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-19-GTCCTTGA-TCGTCTGA_S367_R1_001.fastq.gz 2465-NV-19-GTCCTTGA-TCGTCTGA_S367_R2_001.fastq.gz", "fastq fastq", 10887194400.0, 36290648.0, "2465 NV 19 GTCCTTGA TCGTCTGA S367 R1 001.fastq.gz", "0:150 1:150", "A:3100889552;C:2293240625;G:2475143574;T:3002632683;N:15287966", 150, 150, null, null, 3100889552, 2293240625, 2475143574, 3002632683, 15287966, "SRX5954860", "SRS4865352", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.91599, 0.91172, 0.19536, 0.19246, 0.70806, 0.70798, 0.50256, 0.50214, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52349, "SRR9182355", "SRX5954859", "SRS4865351", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain NAC.ACR NV 20", "NV 20", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:N acetyl L cysteine \u2013 Acrylamide replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: NAC ACR treatment adult male brain", "NV 20", "NV 20", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-20-TGCGTAAC-AGCCTATC_S368_R1_001.fastq.gz 2465-NV-20-TGCGTAAC-AGCCTATC_S368_R2_001.fastq.gz", "fastq fastq", 8599848000.0, 28666160.0, "2465 NV 20 TGCGTAAC AGCCTATC S368 R1 001.fastq.gz", "0:150 1:150", "A:2459848462;C:1811876909;G:1935013502;T:2381063714;N:12045413", 150, 150, null, null, 2459848462, 1811876909, 1935013502, 2381063714, 12045413, "SRX5954859", "SRS4865351", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.90829, 0.91168, 0.1888, 0.18778, 0.71052, 0.70974, 0.50265, 0.50128, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52350, "SRR9182356", "SRX5954858", "SRS4865350", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain ACR NV 15", "NV 15", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:Acrylamide replicate 7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: ACR treatment adult male brain", "NV 15", "NV 15", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-15-CTGTACCA-CACAGACT_S363_R1_001.fastq.gz 2465-NV-15-CTGTACCA-CACAGACT_S363_R2_001.fastq.gz", "fastq fastq", 12883881000.0, 42946270.0, "2465 NV 15 CTGTACCA CACAGACT S363 R1 001.fastq.gz", "0:150 1:150", "A:3671918368;C:2718517333;G:2919934921;T:3555514010;N:17996368", 150, 150, null, null, 3671918368, 2718517333, 2919934921, 3555514010, 17996368, "SRX5954858", "SRS4865350", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.90841, 0.90853, 0.19392, 0.19141, 0.70587, 0.70654, 0.49326, 0.49205, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52351, "SRR9182357", "SRX5954857", "SRS4865349", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain ACR NV 16", "NV 16", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:Acrylamide replicate 8|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: ACR treatment adult male brain", "NV 16", "NV 16", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-16-AGACCTTG-TTACGTGC_S364_R1_001.fastq.gz 2465-NV-16-AGACCTTG-TTACGTGC_S364_R2_001.fastq.gz", "fastq fastq", 9547257000.0, 31824190.0, "2465 NV 16 AGACCTTG TTACGTGC S364 R1 001.fastq.gz", "0:150 1:150", "A:2727492613;C:2021687582;G:2149525733;T:2635174423;N:13376649", 150, 150, null, null, 2727492613, 2021687582, 2149525733, 2635174423, 13376649, "SRX5954857", "SRS4865349", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.91935, 0.91466, 0.19454, 0.19179, 0.70692, 0.70749, 0.49886, 0.5096, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52352, "SRR9182358", "SRX5954856", "SRS4865348", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain NAC.ACR NV 17", "NV 17", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:N acetyl L cysteine \u2013 Acrylamide replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: NAC ACR treatment adult male brain", "NV 17", "NV 17", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-17-AGGATAGC-CCAAGGTT_S365_R1_001.fastq.gz 2465-NV-17-AGGATAGC-CCAAGGTT_S365_R2_001.fastq.gz", "fastq fastq", 10214864100.0, 34049547.0, "2465 NV 17 AGGATAGC CCAAGGTT S365 R1 001.fastq.gz", "0:150 1:150", "A:2930759198;C:2153599072;G:2292844182;T:2823524324;N:14137324", 150, 150, null, null, 2930759198, 2153599072, 2292844182, 2823524324, 14137324, "SRX5954856", "SRS4865348", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.90601, 0.9096, 0.1939, 0.19302, 0.71153, 0.71058, 0.4986, 0.49859, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52353, "SRR9182359", "SRX5954855", "SRS4865346", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain NAC.ACR NV 18", "NV 18", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:N acetyl L cysteine \u2013 Acrylamide replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: NAC ACR treatment adult male brain", "NV 18", "NV 18", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-18-CCTTCCAT-CACGCAAT_S366_R1_001.fastq.gz 2465-NV-18-CCTTCCAT-CACGCAAT_S366_R2_001.fastq.gz", "fastq fastq", 11525333100.0, 38417777.0, "2465 NV 18 CCTTCCAT CACGCAAT S366 R1 001.fastq.gz", "0:150 1:150", "A:3270678875;C:2451086000;G:2608740654;T:3178621310;N:16206261", 150, 150, null, null, 3270678875, 2451086000, 2608740654, 3178621310, 16206261, "SRX5954855", "SRS4865346", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.90965, 0.91093, 0.19965, 0.19785, 0.70707, 0.70751, 0.50506, 0.50301, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52354, "SRR9182360", "SRX5954854", "SRS4865347", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain ACR NV 11", "NV 11", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:Acrylamide replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: ACR treatment adult male brain", "NV 11", "NV 11", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-11-GTACACCT-TCCTCATG_S359_R1_001.fastq.gz 2465-NV-11-GTACACCT-TCCTCATG_S359_R2_001.fastq.gz", "fastq fastq", 9189461700.0, 30631539.0, "2465 NV 11 GTACACCT TCCTCATG S359 R1 001.fastq.gz", "0:150 1:150", "A:2648852788;C:1939379177;G:1999011312;T:2589230521;N:12987902", 150, 150, null, null, 2648852788, 1939379177, 1999011312, 2589230521, 12987902, "SRX5954854", "SRS4865347", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.91673, 0.91678, 0.19869, 0.19589, 0.71279, 0.71108, 0.48443, 0.48705, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52355, "SRR9182361", "SRX5954853", "SRS4865345", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain ACR NV 12", "NV 12", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:Acrylamide replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: ACR treatment adult male brain", "NV 12", "NV 12", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-12-CGGCATTA-GTCAGTCA_S360_R1_001.fastq.gz 2465-NV-12-CGGCATTA-GTCAGTCA_S360_R2_001.fastq.gz", "fastq fastq", 9866562000.0, 32888540.0, "2465 NV 12 CGGCATTA GTCAGTCA S360 R1 001.fastq.gz", "0:150 1:150", "A:2801381823;C:2096538504;G:2245280379;T:2709477444;N:13883850", 150, 150, null, null, 2801381823, 2096538504, 2245280379, 2709477444, 13883850, "SRX5954853", "SRS4865345", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.91095, 0.91237, 0.19276, 0.1915, 0.71212, 0.71147, 0.49114, 0.49659, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52356, "SRR9182362", "SRX5954852", "SRS4865343", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain ACR NV 13", "NV 13", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:Acrylamide replicate 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: ACR treatment adult male brain", "NV 13", "NV 13", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-13-TCGTCTGA-GTCCTTGA_S361_R1_001.fastq.gz 2465-NV-13-TCGTCTGA-GTCCTTGA_S361_R2_001.fastq.gz", "fastq fastq", 10306052700.0, 34353509.0, "2465 NV 13 TCGTCTGA GTCCTTGA S361 R1 001.fastq.gz", "0:150 1:150", "A:2914600925;C:2190104547;G:2374390393;T:2812694857;N:14261978", 150, 150, null, null, 2914600925, 2190104547, 2374390393, 2812694857, 14261978, "SRX5954852", "SRS4865343", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.90694, 0.90932, 0.18903, 0.18749, 0.70968, 0.70891, 0.49997, 0.50056, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52357, "SRR9182363", "SRX5954851", "SRS4865344", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain ACR NV 14", "NV 14", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:Acrylamide replicate 6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: ACR treatment adult male brain", "NV 14", "NV 14", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-14-AGCCTATC-TGCGTAAC_S362_R1_001.fastq.gz 2465-NV-14-AGCCTATC-TGCGTAAC_S362_R2_001.fastq.gz", "fastq fastq", 10331273100.0, 34437577.0, "2465 NV 14 AGCCTATC TGCGTAAC S362 R1 001.fastq.gz", "0:150 1:150", "A:2924091961;C:2225839714;G:2343478200;T:2823411001;N:14452224", 150, 150, null, null, 2924091961, 2225839714, 2343478200, 2823411001, 14452224, "SRX5954851", "SRS4865344", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.91523, 0.91836, 0.18722, 0.18606, 0.70926, 0.70989, 0.4901, 0.49001, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52358, "SRR9182364", "SRX5954850", "SRS4865342", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain ACR NV 9", "NV 9", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:Acrylamide replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: ACR treatment adult male brain", "NV 9", "NV 9", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-9-CGCAACTA-TCGGATTC_S357_R1_001.fastq.gz 2465-NV-9-CGCAACTA-TCGGATTC_S357_R2_001.fastq.gz", "fastq fastq", 11301892800.0, 37672976.0, "2465 NV 9 CGCAACTA TCGGATTC S357 R1 001.fastq.gz", "0:150 1:150", "A:3243365605;C:2381322574;G:2546823051;T:3114598680;N:15782890", 150, 150, null, null, 3243365605, 2381322574, 2546823051, 3114598680, 15782890, "SRX5954850", "SRS4865342", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.90022, 0.90704, 0.20495, 0.20403, 0.71577, 0.71528, 0.49285, 0.5029, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52359, "SRR9182365", "SRX5954849", "SRS4865341", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain ACR NV 10", "NV 10", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:Acrylamide replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: ACR treatment adult male brain", "NV 10", "NV 10", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-10-CGTATCTC-CAAGGTAC_S358_R1_001.fastq.gz 2465-NV-10-CGTATCTC-CAAGGTAC_S358_R2_001.fastq.gz", "fastq fastq", 8971546500.0, 29905155.0, "2465 NV 10 CGTATCTC CAAGGTAC S358 R1 001.fastq.gz", "0:150 1:150", "A:2536960465;C:1929843661;G:2029563929;T:2462734724;N:12443721", 150, 150, null, null, 2536960465, 1929843661, 2029563929, 2462734724, 12443721, "SRX5954849", "SRS4865341", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.91207, 0.91692, 0.1843, 0.1845, 0.71187, 0.71185, 0.49886, 0.49928, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52360, "SRR9182366", "SRX5954848", "SRS4865340", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain Control NV 1", "NV 1", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:Control replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: control adult male brain", "NV 1", "NV 1", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-1-TTACCGAC-CGAATACG_S349_R1_001.fastq.gz 2465-NV-1-TTACCGAC-CGAATACG_S349_R2_001.fastq.gz", "fastq fastq", 10273535700.0, 34245119.0, "2465 NV 1 TTACCGAC CGAATACG S349 R1 001.fastq.gz", "0:150 1:150", "A:2928554067;C:2159492430;G:2335266656;T:2835786931;N:14435616", 150, 150, null, null, 2928554067, 2159492430, 2335266656, 2835786931, 14435616, "SRX5954848", "SRS4865340", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.9087, 0.90313, 0.19787, 0.19441, 0.71756, 0.71709, 0.51109, 0.50869, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52361, "SRR9182367", "SRX5954847", "SRS4865339", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain Control NV 2", "NV 2", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:Control replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: control adult male brain", "NV 2", "NV 2", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-2-AGTGACCT-TCTAGGAG_S350_R1_001.fastq.gz 2465-NV-2-AGTGACCT-TCTAGGAG_S350_R2_001.fastq.gz", "fastq fastq", 11207097900.0, 37356993.0, "2465 NV 2 AGTGACCT TCTAGGAG S350 R1 001.fastq.gz", "0:150 1:150", "A:3148284817;C:2423396873;G:2587025230;T:3032822731;N:15568249", 150, 150, null, null, 3148284817, 2423396873, 2587025230, 3032822731, 15568249, "SRX5954847", "SRS4865339", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.91551, 0.91538, 0.17481, 0.17281, 0.70556, 0.70487, 0.48335, 0.48786, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52362, "SRR9182368", "SRX5954846", "SRS4865338", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain Control NV 3", "NV 3", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:Control replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: control adult male brain", "NV 3", "NV 3", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-3-TCGGATTC-CGCAACTA_S351_R1_001.fastq.gz 2465-NV-3-TCGGATTC-CGCAACTA_S351_R2_001.fastq.gz", "fastq fastq", 12058574400.0, 40195248.0, "2465 NV 3 TCGGATTC CGCAACTA S351 R1 001.fastq.gz", "0:150 1:150", "A:3459397409;C:2538226914;G:2686587266;T:3357533701;N:16829110", 150, 150, null, null, 3459397409, 2538226914, 2686587266, 3357533701, 16829110, "SRX5954846", "SRS4865338", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.91597, 0.90969, 0.20272, 0.19926, 0.71683, 0.71705, 0.50712, 0.51001, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52363, "SRR9182369", "SRX5954845", "SRS4865337", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain Control NV 4", "NV 4", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:Control replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: control adult male brain", "NV 4", "NV 4", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-4-CAAGGTAC-CGTATCTC_S352_R1_001.fastq.gz 2465-NV-4-CAAGGTAC-CGTATCTC_S352_R2_001.fastq.gz", "fastq fastq", 9553550700.0, 31845169.0, "2465 NV 4 CAAGGTAC CGTATCTC S352 R1 001.fastq.gz", "0:150 1:150", "A:2651658029;C:2055962954;G:2305916565;T:2526800154;N:13212998", 150, 150, null, null, 2651658029, 2055962954, 2305916565, 2526800154, 13212998, "SRX5954845", "SRS4865337", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.90798, 0.91396, 0.17694, 0.17825, 0.71033, 0.70922, 0.50819, 0.50573, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52364, "SRR9182370", "SRX5954844", "SRS4865336", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain Control NV 5", "NV 5", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:Control replicate 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: control adult male brain", "NV 5", "NV 5", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-5-TCCTCATG-GTACACCT_S353_R1_001.fastq.gz 2465-NV-5-TCCTCATG-GTACACCT_S353_R2_001.fastq.gz", "fastq fastq", 11521424700.0, 38404749.0, "2465 NV 5 TCCTCATG GTACACCT S353 R1 001.fastq.gz", "0:150 1:150", "A:3258562339;C:2467727220;G:2627261408;T:3152030777;N:15842956", 150, 150, null, null, 3258562339, 2467727220, 2627261408, 3152030777, 15842956, "SRX5954844", "SRS4865336", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.91092, 0.91441, 0.18002, 0.17856, 0.70881, 0.70903, 0.4941, 0.48795, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52365, "SRR9182371", "SRX5954843", "SRS4865335", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain Control NV 6", "NV 6", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:Control replicate 6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: control adult male brain", "NV 6", "NV 6", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-6-GTCAGTCA-CGGCATTA_S354_R1_001.fastq.gz 2465-NV-6-GTCAGTCA-CGGCATTA_S354_R2_001.fastq.gz", "fastq fastq", 9803104500.0, 32677015.0, "2465 NV 6 GTCAGTCA CGGCATTA S354 R1 001.fastq.gz", "0:150 1:150", "A:2779645686;C:2103402652;G:2218294150;T:2688098948;N:13663064", 150, 150, null, null, 2779645686, 2103402652, 2218294150, 2688098948, 13663064, "SRX5954843", "SRS4865335", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.9114, 0.91625, 0.1819, 0.18102, 0.70611, 0.70644, 0.48862, 0.48985, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52366, "SRR9182372", "SRX5954842", "SRS4865334", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain Control NV 7", "NV 7", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:Control replicate 7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: control adult male brain", "NV 7", "NV 7", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-7-CGAATACG-TTACCGAC_S355_R1_001.fastq.gz 2465-NV-7-CGAATACG-TTACCGAC_S355_R2_001.fastq.gz", "fastq fastq", 9872477100.0, 32908257.0, "2465 NV 7 CGAATACG TTACCGAC S355 R1 001.fastq.gz", "0:150 1:150", "A:2786558009;C:2110864680;G:2279325984;T:2682111265;N:13617162", 150, 150, null, null, 2786558009, 2110864680, 2279325984, 2682111265, 13617162, "SRX5954842", "SRS4865334", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.90855, 0.91239, 0.1835, 0.18248, 0.7125, 0.7108, 0.49696, 0.49654, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [52367, "SRR9182373", "SRX5954841", "SRS4865333", "SRP200180", "PRJNA545942", "Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain", "PRJNA545942", "Other", "Acrylamide is a recognized carcinogen that has strong neurotoxic effectseffects in humans and in experimental animals  although the molecular mechanisms underlying these neurotoxic effects are not completely understood. We studied acrylamide neurotoxicity in adult zebrafish using an integrated approach that included biochemical  transcriptomic  proteomic and metabolomic data. Brain samples from exposed and control zebrafish were subjected to proton NMR for metabolomic analysis  to MALDI TOF mass spectrometry for proteome analysis  and to high throughput RNA sequencing for transcriptomic analysis. We detected the formation of acrylamide adducts with thiol groups in the brain metabolome  and the accumulation of acrylamide conjugates and propionamide adducts in Cys residues of proteins. These combined effects resulted in a quasi complete depletion of glutathione and to the inactivation of different components of the thioredoxin system. Multi omic functional analyses identified microtubules  thioredoxin related proteins  transmembrane transport  redox metabolism and catalytic activity  as the cellular functions significantly altered by acrylamide in the fish brain. We propose that the combined loss of function of both redox metabolism related systems configure a perfect storm that explains many acrylamide neurotoxic effects  like the dysregulation of genes related to microtubules  presynaptic vesicle alteration  and behavioral alterations. We further propose an Adverse Outcome Pathway of acrylamide neurotoxicity  connecting the different toxic effects across different levels of organization  from molecular interactions to behavioral changes. Our mechanistical approach may help developing new treatments against the neurotoxic effects of acrylamideand of other neurotoxicants that may share its toxic mode of action.", null, null, null, "ZF Brain Control NV 8", "NV 8", null, "strain:WT|dev stage:Adult|sex:male|tissue:Brain|treatment:Control replicate 8|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: control adult male brain", "NV 8", "NV 8", "Zebrafish brain RNA was sent to the Vanderbilt Technologies for Advanced Genomics Vanderbilt University  Nashville  TN for library preparation and sequencing on the Illumina Novaseq platform", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP200180", null, null, "2465-NV-8-TCTAGGAG-AGTGACCT_S356_R1_001.fastq.gz 2465-NV-8-TCTAGGAG-AGTGACCT_S356_R2_001.fastq.gz", "fastq fastq", 8271516900.0, 27571723.0, "2465 NV 8 TCTAGGAG AGTGACCT S356 R1 001.fastq.gz", "0:150 1:150", "A:2342223288;C:1770487584;G:1884385861;T:2263052869;N:11367298", 150, 150, null, null, 2342223288, 1770487584, 1884385861, 2263052869, 11367298, "SRX5954841", "SRS4865333", "SRA893242", "Mississippi State University|Institute for Genomics, Biocomputing & Biotechnolo", "Mississippi State University", 2, 0.91345, 0.91392, 0.17601, 0.17437, 0.70985, 0.70962, 0.49294, 0.49772, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-03", "Adult", "Adult", "Brain", "Nervous System"], [58533, "SRR11355387", "SRX7957249", "SRS6343356", "SRP253408", "PRJNA613558", "Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture", "PRJNA613558", "Other", "As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease  the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation  adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study  combined with antibiotics bioaccumulated in ovary  we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish  and thus affect egg production and survival. Therefore  ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0  1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.", null, null, null, "C2 3", "C2 3", null, "strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C2 320200327", "C2 320200327", "RNA seq of zebrafish in different conditions", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP253408", null, null, "C2_3_1.fq.gz C2_3_2.fq.gz", "fastq fastq", 6857650800.0, 45717672.0, "C2 3 1.fq.gz", "0:150 1:150", "A:1826466263;C:1599272942;G:1580689630;T:1851144875;N:77090", 150, 150, null, null, 1826466263, 1599272942, 1580689630, 1851144875, 77090, "SRX7957249", "SRS6343356", "SRA1056819", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.93222, null, 0.02854, null, 0.75138, null, 0.50759, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-20", "Undetermined", "Adult", "Gonad", "Reproductive System"], [58534, "SRR11355388", "SRX7957248", "SRS6343355", "SRP253408", "PRJNA613558", "Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture", "PRJNA613558", "Other", "As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease  the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation  adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study  combined with antibiotics bioaccumulated in ovary  we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish  and thus affect egg production and survival. Therefore  ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0  1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.", null, null, null, "C2 2", "C2 2", null, "strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C2 220200326", "C2 220200326", "RNA seq of zebrafish in different conditions", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP253408", null, null, "C2_2_1.fq.gz C2_2_2.fq.gz", "fastq fastq", 6859954800.0, 45733032.0, "C2 2 1.fq.gz", "0:150 1:150", "A:1836618967;C:1591135182;G:1572318102;T:1859806048;N:76501", 150, 150, null, null, 1836618967, 1591135182, 1572318102, 1859806048, 76501, "SRX7957248", "SRS6343355", "SRA1056819", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.93237, null, 0.03248, null, 0.74663, null, 0.5081, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-20", "Undetermined", "Adult", "Gonad", "Reproductive System"], [58535, "SRR11355389", "SRX7957247", "SRS6343354", "SRP253408", "PRJNA613558", "Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture", "PRJNA613558", "Other", "As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease  the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation  adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study  combined with antibiotics bioaccumulated in ovary  we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish  and thus affect egg production and survival. Therefore  ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0  1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.", null, null, null, "C2 1", "C2 1", null, "strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C2 120200325", "C2 120200325", "RNA seq of zebrafish in different conditions", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP253408", null, null, "C2_1_1.fq.gz C2_1_2.fq.gz", "fastq fastq", 6618974400.0, 44126496.0, "C2 1 1.fq.gz", "0:150 1:150", "A:1774116288;C:1533828286;G:1511526952;T:1799423408;N:79466", 150, 150, null, null, 1774116288, 1533828286, 1511526952, 1799423408, 79466, "SRX7957247", "SRS6343354", "SRA1056819", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.9326, null, 0.02973, null, 0.75426, null, 0.50678, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-20", "Undetermined", "Adult", "Gonad", "Reproductive System"], [58536, "SRR11355390", "SRX7957246", "SRS6343353", "SRP253408", "PRJNA613558", "Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture", "PRJNA613558", "Other", "As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease  the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation  adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study  combined with antibiotics bioaccumulated in ovary  we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish  and thus affect egg production and survival. Therefore  ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0  1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.", null, null, null, "C1 3", "C1 3", null, "strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C1 320200324", "C1 320200324", "RNA seq of zebrafish in different conditions", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP253408", null, null, "C1_3_1.fq.gz C1_3_2.fq.gz", "fastq fastq", 6837729600.0, 45584864.0, "C1 3 1.fq.gz", "0:150 1:150", "A:1831266308;C:1587032733;G:1565071069;T:1853950421;N:409069", 150, 150, null, null, 1831266308, 1587032733, 1565071069, 1853950421, 409069, "SRX7957246", "SRS6343353", "SRA1056819", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.93541, null, 0.03212, null, 0.74681, null, 0.50268, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-20", "Undetermined", "Adult", "Gonad", "Reproductive System"], [58537, "SRR11355391", "SRX7957245", "SRS6343352", "SRP253408", "PRJNA613558", "Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture", "PRJNA613558", "Other", "As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease  the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation  adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study  combined with antibiotics bioaccumulated in ovary  we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish  and thus affect egg production and survival. Therefore  ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0  1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.", null, null, null, "C1 2", "C1 2", null, "strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C1 220200323", "C1 220200323", "RNA seq of zebrafish in different conditions", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP253408", null, null, "C1_2_2.fq.gz C1_2_1.fq.gz", "fastq fastq", 6860328000.0, 45735520.0, "C1 2 1.fq.gz", "0:150 1:150", "A:1838176072;C:1591277709;G:1569605888;T:1861063734;N:204597", 150, 150, null, null, 1838176072, 1591277709, 1569605888, 1861063734, 204597, "SRX7957245", "SRS6343352", "SRA1056819", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.93763, null, 0.033, null, 0.74617, null, 0.50287, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-20", "Undetermined", "Adult", "Gonad", "Reproductive System"], [58538, "SRR11355392", "SRX7957244", "SRS6343351", "SRP253408", "PRJNA613558", "Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture", "PRJNA613558", "Other", "As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease  the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation  adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study  combined with antibiotics bioaccumulated in ovary  we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish  and thus affect egg production and survival. Therefore  ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0  1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.", null, null, null, "C1 1", "C1 1", null, "strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C1 120200322", "C1 120200322", "RNA seq of zebrafish in different conditions", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP253408", null, null, "C1_1_1.fq.gz C1_1_2.fq.gz", "fastq fastq", 6865547700.0, 45770318.0, "C1 1 1.fq.gz", "0:150 1:150", "A:1841774713;C:1591288582;G:1570400871;T:1861867728;N:215806", 150, 150, null, null, 1841774713, 1591288582, 1570400871, 1861867728, 215806, "SRX7957244", "SRS6343351", "SRA1056819", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.93567, null, 0.03152, null, 0.74653, null, 0.50239, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-20", "Undetermined", "Adult", "Gonad", "Reproductive System"], [58539, "SRR11355393", "SRX7957243", "SRS6343350", "SRP253408", "PRJNA613558", "Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture", "PRJNA613558", "Other", "As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease  the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation  adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study  combined with antibiotics bioaccumulated in ovary  we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish  and thus affect egg production and survival. Therefore  ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0  1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.", null, null, null, "C0 3", "C0 3", null, "strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C0 320200321", "C0 320200321", "RNA seq of zebrafish in different conditions", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP253408", null, null, "C0_3_1.fq.gz C0_3_2.fq.gz", "fastq fastq", 6824622600.0, 45497484.0, "C0 3 1.fq.gz", "0:150 1:150", "A:1833660953;C:1578510104;G:1558095174;T:1854128169;N:228200", 150, 150, null, null, 1833660953, 1578510104, 1558095174, 1854128169, 228200, "SRX7957243", "SRS6343350", "SRA1056819", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.93758, null, 0.0323, null, 0.75024, null, 0.50852, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-20", "Undetermined", "Adult", "Gonad", "Reproductive System"], [58540, "SRR11355394", "SRX7957242", "SRS6343349", "SRP253408", "PRJNA613558", "Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture", "PRJNA613558", "Other", "As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease  the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation  adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study  combined with antibiotics bioaccumulated in ovary  we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish  and thus affect egg production and survival. Therefore  ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0  1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.", null, null, null, "C0 2", "C0 2", null, "strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C0 220200320", "C0 220200320", "RNA seq of zebrafish in different conditions", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP253408", null, null, "C0_2_2.fq.gz C0_2_1.fq.gz", "fastq fastq", 6819326400.0, 45462176.0, "C0 2 1.fq.gz", "0:150 1:150", "A:1837661215;C:1571877614;G:1550458835;T:1859103408;N:225328", 150, 150, null, null, 1837661215, 1571877614, 1550458835, 1859103408, 225328, "SRX7957242", "SRS6343349", "SRA1056819", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.93697, null, 0.0339, null, 0.74793, null, 0.5035, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-20", "Undetermined", "Adult", "Gonad", "Reproductive System"], [58541, "SRR11355395", "SRX7957241", "SRS6343348", "SRP253408", "PRJNA613558", "Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture", "PRJNA613558", "Other", "As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease  the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation  adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study  combined with antibiotics bioaccumulated in ovary  we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish  and thus affect egg production and survival. Therefore  ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0  1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.", null, null, null, "C0 1", "C0 1", null, "strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C0 120200319", "C0 120200319", "RNA seq of zebrafish in different conditions", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP253408", null, null, "C0_1_1.fq.gz C0_1_2.fq.gz", "fastq fastq", 7030804800.0, 46872032.0, "C0 1 1.fq.gz", "0:150 1:150", "A:1891469955;C:1624531422;G:1603124564;T:1911444454;N:234405", 150, 150, null, null, 1891469955, 1624531422, 1603124564, 1911444454, 234405, "SRX7957241", "SRS6343348", "SRA1056819", "Southern University of Science and Technology|School of Environmental Science and Engineering", "Southern University of Science and Technology", 1, 0.93519, null, 0.0328, null, 0.74602, null, 0.48272, null, 150, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-20", "Undetermined", "Adult", "Gonad", "Reproductive System"], [59629, "SRR12023698", "SRX8555537", "SRS6849262", "SRP267510", "PRJNA638724", "Danio rerio Transcriptome or Gene expression", "PRJNA638724", "Other", "Inflammation is a constant companion of Non Alcoholic Fatty Liver Disease NAFLD. However  it is generally considered to be a consequence rather than cause. Using a transgenic model we demonstrate that chronic systemic exposure to human IL6 causes intrahepatic triglyceride accumulation in the zebrafish. The inflammation based zebrafish model for NAFLD has a transcriptome signature distinct from the diet based NAFLD models. Instead  a marked deregulation of glycolysis/gluconeogenesis pathway  specifically a robust down regulation of the glycolytic enzyme aldolase b  was evident in both transcriptomics and proteomics studies of liver exposed to IL6. Metabolomics of the zebrafish liver showed accumulation of hexose monophosphates. This is reminiscent of patients of the genetic disease Hereditary Fructose Intolerance HFI caused by aldolase B deficiency and HFI patients appear to have a higher propensity to develop fatty liver disease than controls.In Caucasians NAFLD is generally associated with obesity. However  in the South Asian population  lean males have been noted to develop NAFLD. Asian Indians also seem to have higher basal circulating IL6. Our inflammation based zebrafish transgenic might model this emerging category of NAFLD better than the conventional high fat diet based NAFLD animal models. Our study suggests that inflammation driven repression of aldolase b may be a novel mechanism for accumulation of intrahepatic triglyceride  especially in obesity independent NAFLD.", null, null, null, "Model organism or animal sample from Danio rerio", "IL6 Female 1", null, "strain:NA|dev stage:Adult|sex:female|tissue:Liver|genotype:Tg myl7:GAL4 VP16  myl7:cerulean::UAS:HsaIL6  myl7:cherry|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "IL6 Female 1", "Illumina 19", "Illumina 19", "RNA Sample from Liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP267510", null, null, "CSL007_R1.fastq CSL007_R2.fastq", "fastq fastq", 18211649100.0, 60705497.0, "CSL007 R1.fastq", "0:150 1:150", "A:4786490131;C:4456957567;G:4686466847;T:4280762656;N:971899", 150, 150, null, null, 4786490131, 4456957567, 4686466847, 4280762656, 971899, "SRX8555537", "SRS6849262", "SRA1087578", "CSIR-Institute of Genomics and Integrative Biology|Biological Science", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.89432, 0.88762, 0.23097, 0.22341, 0.78585, 0.78555, 0.5675, 0.56744, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2020-06-16", "Adult", "Adult", "Liver", "Liver and Biliary System"], [59630, "SRR12023699", "SRX8555536", "SRS6849261", "SRP267510", "PRJNA638724", "Danio rerio Transcriptome or Gene expression", "PRJNA638724", "Other", "Inflammation is a constant companion of Non Alcoholic Fatty Liver Disease NAFLD. However  it is generally considered to be a consequence rather than cause. Using a transgenic model we demonstrate that chronic systemic exposure to human IL6 causes intrahepatic triglyceride accumulation in the zebrafish. The inflammation based zebrafish model for NAFLD has a transcriptome signature distinct from the diet based NAFLD models. Instead  a marked deregulation of glycolysis/gluconeogenesis pathway  specifically a robust down regulation of the glycolytic enzyme aldolase b  was evident in both transcriptomics and proteomics studies of liver exposed to IL6. Metabolomics of the zebrafish liver showed accumulation of hexose monophosphates. This is reminiscent of patients of the genetic disease Hereditary Fructose Intolerance HFI caused by aldolase B deficiency and HFI patients appear to have a higher propensity to develop fatty liver disease than controls.In Caucasians NAFLD is generally associated with obesity. However  in the South Asian population  lean males have been noted to develop NAFLD. Asian Indians also seem to have higher basal circulating IL6. Our inflammation based zebrafish transgenic might model this emerging category of NAFLD better than the conventional high fat diet based NAFLD animal models. Our study suggests that inflammation driven repression of aldolase b may be a novel mechanism for accumulation of intrahepatic triglyceride  especially in obesity independent NAFLD.", null, null, null, "Model organism or animal sample from Danio rerio", "Control Female 3", null, "strain:NA|dev stage:Adult|sex:female|tissue:Liver|genotype:Tg myl7:GAL4 VP16  myl7:cerulean|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Control Female 3", "Illumina 17", "Illumina 17", "RNA Sample from Liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP267510", null, null, "CSL0026_ACTTGA_R1.fastq CSL0026_ACTTGA_R2.fastq", "fastq fastq", 20723429400.0, 69078098.0, "CSL0026 ACTTGA R1.fastq", "0:150 1:150", "A:5402976575;C:4999160043;G:4897109379;T:5421795577;N:2387826", 150, 150, null, null, 5402976575, 4999160043, 4897109379, 5421795577, 2387826, "SRX8555536", "SRS6849261", "SRA1087578", "CSIR-Institute of Genomics and Integrative Biology|Biological Science", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.95138, 0.93284, 0.09475, 0.08651, 0.90368, 0.90721, 0.12777, 0.12828, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2020-06-16", "Adult", "Adult", "Liver", "Liver and Biliary System"], [59631, "SRR12023700", "SRX8555535", "SRS6849260", "SRP267510", "PRJNA638724", "Danio rerio Transcriptome or Gene expression", "PRJNA638724", "Other", "Inflammation is a constant companion of Non Alcoholic Fatty Liver Disease NAFLD. However  it is generally considered to be a consequence rather than cause. Using a transgenic model we demonstrate that chronic systemic exposure to human IL6 causes intrahepatic triglyceride accumulation in the zebrafish. The inflammation based zebrafish model for NAFLD has a transcriptome signature distinct from the diet based NAFLD models. Instead  a marked deregulation of glycolysis/gluconeogenesis pathway  specifically a robust down regulation of the glycolytic enzyme aldolase b  was evident in both transcriptomics and proteomics studies of liver exposed to IL6. Metabolomics of the zebrafish liver showed accumulation of hexose monophosphates. This is reminiscent of patients of the genetic disease Hereditary Fructose Intolerance HFI caused by aldolase B deficiency and HFI patients appear to have a higher propensity to develop fatty liver disease than controls.In Caucasians NAFLD is generally associated with obesity. However  in the South Asian population  lean males have been noted to develop NAFLD. Asian Indians also seem to have higher basal circulating IL6. Our inflammation based zebrafish transgenic might model this emerging category of NAFLD better than the conventional high fat diet based NAFLD animal models. Our study suggests that inflammation driven repression of aldolase b may be a novel mechanism for accumulation of intrahepatic triglyceride  especially in obesity independent NAFLD.", null, null, null, "Model organism or animal sample from Danio rerio", "Control Female 2", null, "strain:NA|dev stage:Adult|sex:female|tissue:Liver|genotype:Tg myl7:GAL4 VP16  myl7:cerulean|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Control Female 2", "Illumina 15", "Illumina 15", "RNA Sample from Liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP267510", null, null, "CSL0025_CAGATC_R2.fastq CSL0025_CAGATC_R1.fastq", "fastq fastq", 11660340300.0, 38867801.0, "CSL0025 CAGATC R1.fastq", "0:150 1:150", "A:3029714430;C:2832126451;G:2769224528;T:3027949176;N:1325715", 150, 150, null, null, 3029714430, 2832126451, 2769224528, 3027949176, 1325715, "SRX8555535", "SRS6849260", "SRA1087578", "CSIR-Institute of Genomics and Integrative Biology|Biological Science", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.94173, 0.92715, 0.09343, 0.08719, 0.89457, 0.89881, 0.1798, 0.17459, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2020-06-16", "Adult", "Adult", "Liver", "Liver and Biliary System"], [59632, "SRR12023701", "SRX8555534", "SRS6849259", "SRP267510", "PRJNA638724", "Danio rerio Transcriptome or Gene expression", "PRJNA638724", "Other", "Inflammation is a constant companion of Non Alcoholic Fatty Liver Disease NAFLD. However  it is generally considered to be a consequence rather than cause. Using a transgenic model we demonstrate that chronic systemic exposure to human IL6 causes intrahepatic triglyceride accumulation in the zebrafish. The inflammation based zebrafish model for NAFLD has a transcriptome signature distinct from the diet based NAFLD models. Instead  a marked deregulation of glycolysis/gluconeogenesis pathway  specifically a robust down regulation of the glycolytic enzyme aldolase b  was evident in both transcriptomics and proteomics studies of liver exposed to IL6. Metabolomics of the zebrafish liver showed accumulation of hexose monophosphates. This is reminiscent of patients of the genetic disease Hereditary Fructose Intolerance HFI caused by aldolase B deficiency and HFI patients appear to have a higher propensity to develop fatty liver disease than controls.In Caucasians NAFLD is generally associated with obesity. However  in the South Asian population  lean males have been noted to develop NAFLD. Asian Indians also seem to have higher basal circulating IL6. Our inflammation based zebrafish transgenic might model this emerging category of NAFLD better than the conventional high fat diet based NAFLD animal models. Our study suggests that inflammation driven repression of aldolase b may be a novel mechanism for accumulation of intrahepatic triglyceride  especially in obesity independent NAFLD.", null, null, null, "Model organism or animal sample from Danio rerio", "Control Female 1", null, "strain:NA|dev stage:Adult|sex:female|tissue:Liver|genotype:Tg myl7:GAL4 VP16  myl7:cerulean|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Control Female 1", "Illumina 13", "Illumina 13", "RNA Sample from Liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP267510", null, null, "CSL006_R1.fastq CSL006_R2.fastq", "fastq fastq", 26822412600.0, 89408042.0, "CSL006 R1.fastq", "0:150 1:150", "A:6857894757;C:6829803951;G:7088582304;T:6044701966;N:1429622", 150, 150, null, null, 6857894757, 6829803951, 7088582304, 6044701966, 1429622, "SRX8555534", "SRS6849259", "SRA1087578", "CSIR-Institute of Genomics and Integrative Biology|Biological Science", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.92566, 0.9196, 0.13976, 0.13479, 0.93415, 0.93247, 0.30814, 0.3021, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2020-06-16", "Adult", "Adult", "Liver", "Liver and Biliary System"], [59633, "SRR12023702", "SRX8555533", "SRS6849258", "SRP267510", "PRJNA638724", "Danio rerio Transcriptome or Gene expression", "PRJNA638724", "Other", "Inflammation is a constant companion of Non Alcoholic Fatty Liver Disease NAFLD. However  it is generally considered to be a consequence rather than cause. Using a transgenic model we demonstrate that chronic systemic exposure to human IL6 causes intrahepatic triglyceride accumulation in the zebrafish. The inflammation based zebrafish model for NAFLD has a transcriptome signature distinct from the diet based NAFLD models. Instead  a marked deregulation of glycolysis/gluconeogenesis pathway  specifically a robust down regulation of the glycolytic enzyme aldolase b  was evident in both transcriptomics and proteomics studies of liver exposed to IL6. Metabolomics of the zebrafish liver showed accumulation of hexose monophosphates. This is reminiscent of patients of the genetic disease Hereditary Fructose Intolerance HFI caused by aldolase B deficiency and HFI patients appear to have a higher propensity to develop fatty liver disease than controls.In Caucasians NAFLD is generally associated with obesity. However  in the South Asian population  lean males have been noted to develop NAFLD. Asian Indians also seem to have higher basal circulating IL6. Our inflammation based zebrafish transgenic might model this emerging category of NAFLD better than the conventional high fat diet based NAFLD animal models. 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