metadata: run_metadata: 41 rows where experiment.library_selection = "RANDOM PCR", experiment.library_source = "TRANSCRIPTOMIC" and tissue

41 rows where experiment.library_selection = "RANDOM PCR", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Liver"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.description	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
48033	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.	Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L and livers were sampled and pooled		PHE3d.3	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	RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day	PHE3d.3	PHE3d.3	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP136856	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	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	China	2018-03-31	Adult	Adult	Liver	Liver and Biliary System
48034	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.	Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L and livers were sampled and pooled		PHE7d.1	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	RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day	PHE7d.1	PHE7d.1	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP136856	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	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	China	2018-03-31	Adult	Adult	Liver	Liver and Biliary System
48035	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.	Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L and livers were sampled and pooled		PHE1d.2	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	RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day	PHE1d.2	PHE1d.2	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP136856	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	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	China	2018-03-31	Adult	Adult	Liver	Liver and Biliary System
48036	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.	Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L and livers were sampled and pooled		PHE1d.3	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	RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day	PHE1d.3	PHE1d.3	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP136856	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	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	China	2018-03-31	Adult	Adult	Liver	Liver and Biliary System
48037	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.	Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L and livers were sampled and pooled		PHE3d.1	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	RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day	PHE3d.1	PHE3d.1	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP136856	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	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	China	2018-03-31	Adult	Adult	Liver	Liver and Biliary System
48038	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.	Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L and livers were sampled and pooled		PHE3d.2	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	RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day	PHE3d.2	PHE3d.2	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP136856	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	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	China	2018-03-31	Adult	Adult	Liver	Liver and Biliary System
48039	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. Our findings could present foundation for further study on molecular mechanism responsible for zebrafish's responses to phenanthrene exposure.	Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L and livers were sampled and pooled		PHE0d.1	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 1\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult male and female without xxx exposure	PHE0d.1	PHE0d.1	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP136856	PHE0d_1_2.fq.gz PHE0d_1_1.fq.gz	fastq fastq	7853933100.0	26179777.0	PHE0d 1 2.fq.gz	0:150 1:150	A:2041706651;C:1888763231;G:1884281701;T:2035607198;N:3574319	150	150	2041706651	1888763231	1884281701	2035607198	3574319	SRX3869071	SRS3112046	SRA678027	Pearl River Fisheries Research Institute, CAFS\|Fisheries environmental protection laboratory	Pearl River Fisheries Research Institute, CAFS	2	0.94164	0.94393	0.02233	0.0224	0.76625	0.77356	0.30965	0.2981	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2018-03-31	Adult	Adult	Liver	Liver and Biliary System
48040	48040	SRR6921822	SRX3869070	SRS3112045	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.	Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L and livers were sampled and pooled		PHE0d.2	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 2\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: adult male and female without xxx exposure	PHE0d.2	PHE0d.2	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP136856	PHE0d_2_2.fq.gz	fastq	3627859350.0	24185729.0	PHE0d 2 2.fq.gz										SRX3869070	SRS3112045	SRA678027	Pearl River Fisheries Research Institute, CAFS\|Fisheries environmental protection laboratory	Pearl River Fisheries Research Institute, CAFS	1	0.87829		0.02367		0.8213		0.29999		150		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2018-03-31	Adult	Adult	Liver	Liver and Biliary System
48041	48041	SRR6921823	SRX3869069	SRS3112044	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.	Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L and livers were sampled and pooled		PHE0d.3	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	RNA Seq of Danio rerio: adult male and female without xxx exposure	PHE0d.3	PHE0d.3	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP136856	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	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		0.0274		0.76031		0.35099		150		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2018-03-31	Adult	Adult	Liver	Liver and Biliary System
48042	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.	Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L and livers were sampled and pooled		PHE1d.1	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	RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day	PHE1d.1	PHE1d.1	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP136856	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	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	China	2018-03-31	Adult	Adult	Liver	Liver and Biliary System
48043	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.	Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L and livers were sampled and pooled		PHE7d.2	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	RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day	PHE7d.2	PHE7d.2	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP136856	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	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	China	2018-03-31	Adult	Adult	Liver	Liver and Biliary System
48044	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.	Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L and livers were sampled and pooled		PHE7d.3	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	RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day	PHE7d.3	PHE7d.3	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP136856	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	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	China	2018-03-31	Adult	Adult	Liver	Liver and Biliary System
48045	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.	Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L and livers were sampled and pooled		PHE15d.1	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	RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day	PHE15d.1	PHE15d.1	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP136856	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	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	China	2018-03-31	Adult	Adult	Liver	Liver and Biliary System
48046	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.	Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L and livers were sampled and pooled		PHE15d.2	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	RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day	PHE15d.2	PHE15d.2	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP136856	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	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	China	2018-03-31	Adult	Adult	Liver	Liver and Biliary System
48047	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.	Fish in trplicate were anaesthetized with MS 222 at the dose of 10 mg/L and livers were sampled and pooled		PHE15d.3	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	RNA Seq of Danio rerio: adult male and female exposed to phenanthrene for xxx day	PHE15d.3	PHE15d.3	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP136856	PHE15d_3_1.fq.gz PHE15d_3_2.fq.gz	fastq fastq	7768190100.0	25893967.0	PHE15d 3 2.fq.gz	0:150 1:150	A:2003796503;C:1879716153;G:1873169874;T:2006471079;N:5036491	150	150	2003796503	1879716153	1873169874	2006471079	5036491	SRX3869063	SRS3112038	SRA678027	Pearl River Fisheries Research Institute, CAFS\|Fisheries environmental protection laboratory	Pearl River Fisheries Research Institute, CAFS	2	0.92663	0.92862	0.05515	0.05537	0.67915	0.6886	0.52556	0.52171	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2018-03-31	Adult	Adult	Liver	Liver and Biliary System
52296	52296	SRR9159929	SRX5933020	SRS4846227	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.			t3	strain:Transgenic\|age:1year\|dev stage:adult\|sex:female\|tissue:liver\|disease stg:0hpd\|Replicate:biological replicate 2\|BioSampleModel:Model organism or animal	t3 rep2	t3 rep2	t3 rep2	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP199854	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	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	India	2019-05-30	Adult	Adult	Liver	Liver and Biliary System
52297	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.			t3 rep1	strain:Transgenic\|age:1year\|dev stage:adult\|sex:female\|tissue:liver\|disease stg:0hpd\|Replicate:biological replicate 1\|BioSampleModel:Model organism or animal	t3 rep1	t3 rep1	t3 rep1	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP199854	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	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	India	2019-05-30	Adult	Adult	Liver	Liver and Biliary System
52298	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.			t0	strain:Transgenic\|age:1year\|dev stage:adult\|sex:female\|tissue:liver\|disease stg:untreated\|Replicate:biological replicate 2\|BioSampleModel:Model organism or animal	t0 rep2	t0 rep2	t0 rep2	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP199854	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	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	India	2019-05-30	Adult	Adult	Liver	Liver and Biliary System
52299	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.			t0 rep1	strain:Transgenic\|age:1year\|dev stage:adult\|sex:female\|tissue:liver\|disease stg:untreated\|Replicate:biological replicate 1\|BioSampleModel:Model organism or animal	t0 rep1	t0 rep1	t0 rep1	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP199854	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	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	India	2019-05-30	Adult	Adult	Liver	Liver and Biliary System
52300	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.			t27	strain:Transgenic\|age:1year\|dev stage:adult\|sex:female\|tissue:liver\|disease stg:24hpd\|Replicate:biological replicate 2\|BioSampleModel:Model organism or animal	t27 rep2	t27 rep2	t27 rep2	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP199854	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	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	India	2019-05-30	Adult	Adult	Liver	Liver and Biliary System
52301	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.			t27 rep1	strain:Transgenic\|age:1year\|dev stage:adult\|sex:female\|tissue:liver\|disease stg:24hpd\|Replicate:biological replicate 1\|BioSampleModel:Model organism or animal	t27 rep1	t27 rep1	t27 rep1	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP199854	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	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	India	2019-05-30	Adult	Adult	Liver	Liver and Biliary System
52302	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.			t15	strain:Transgenic\|age:1year\|dev stage:adult\|sex:female\|tissue:liver\|disease stg:12hpd\|Replicate:biological replicate 2\|BioSampleModel:Model organism or animal	t15 rep2	t15 rep2	t15 rep2	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP199854	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	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	India	2019-05-30	Adult	Adult	Liver	Liver and Biliary System
52303	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.			t15 rep1	strain:Transgenic\|age:1year\|dev stage:adult\|sex:female\|tissue:liver\|disease stg:12hpd\|Replicate:biological replicate 1\|BioSampleModel:Model organism or animal	t15 rep1	t15 rep1	t15 rep1	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP199854	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	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	India	2019-05-30	Adult	Adult	Liver	Liver and Biliary System
52304	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.			t99	strain:Transgenic\|age:1year\|dev stage:adult\|sex:female\|tissue:liver\|disease stg:4dpd\|Replicate:biological replicate 2\|BioSampleModel:Model organism or animal	t99 rep2	t99 rep2	t99 rep2	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP199854	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	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	India	2019-05-30	Adult	Adult	Liver	Liver and Biliary System
52305	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.			t99 rep1	strain:Transgenic\|age:1year\|dev stage:adult\|sex:female\|tissue:liver\|disease stg:4dpd\|Replicate:biological replicate 1\|BioSampleModel:Model organism or animal	t99 rep1	t99 rep1	t99 rep1	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP199854	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	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	India	2019-05-30	Adult	Adult	Liver	Liver and Biliary System
52306	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.			t147	strain:Transgenic\|age:1year\|dev stage:adult\|sex:female\|tissue:liver\|disease stg:6dpd\|Replicate:biological replicate 2\|BioSampleModel:Model organism or animal	t147 rep2	t147 rep2	t147 rep2	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP199854	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	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	India	2019-05-30	Adult	Adult	Liver	Liver and Biliary System
52307	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.			t147 rep1	strain:Transgenic\|age:1year\|dev stage:adult\|sex:female\|tissue:liver\|disease stg:6dpd\|Replicate:biological replicate 1\|BioSampleModel:Model organism or animal	t147 rep1	t147 rep1	t147 rep1	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP199854	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	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	India	2019-05-30	Adult	Adult	Liver	Liver and Biliary System
52308	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.			t195	strain:Transgenic\|age:1year\|dev stage:adult\|sex:female\|tissue:liver\|disease stg:8dpd\|Replicate:biological replicate 2\|BioSampleModel:Model organism or animal	t195 rep2	t195 rep2	t195 rep2	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP199854	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	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	India	2019-05-30	Adult	Adult	Liver	Liver and Biliary System
52309	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.			t195 rep1	strain:Transgenic\|age:1year\|dev stage:adult\|sex:female\|tissue:liver\|disease stg:8dpd\|Replicate:biological replicate 1\|BioSampleModel:Model organism or animal	t195 rep1	t195 rep1	t195 rep1	Random PCR	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP199854	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	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	India	2019-05-30	Adult	Adult	Liver	Liver and Biliary System
59629	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.		Model organism or animal sample from Danio rerio	IL6 Female 1	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	IL6 Female 1	Illumina 19	Illumina 19	RNA Sample from Liver	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP267510	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	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	India	2020-06-16	Adult	Adult	Liver	Liver and Biliary System
59630	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.		Model organism or animal sample from Danio rerio	Control Female 3	strain:NA\|dev stage:Adult\|sex:female\|tissue:Liver\|genotype:Tg myl7:GAL4 VP16 myl7:cerulean\|BioSampleModel:Model organism or animal	Control Female 3	Illumina 17	Illumina 17	RNA Sample from Liver	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP267510	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	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	India	2020-06-16	Adult	Adult	Liver	Liver and Biliary System
59631	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.		Model organism or animal sample from Danio rerio	Control Female 2	strain:NA\|dev stage:Adult\|sex:female\|tissue:Liver\|genotype:Tg myl7:GAL4 VP16 myl7:cerulean\|BioSampleModel:Model organism or animal	Control Female 2	Illumina 15	Illumina 15	RNA Sample from Liver	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP267510	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	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	India	2020-06-16	Adult	Adult	Liver	Liver and Biliary System
59632	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.		Model organism or animal sample from Danio rerio	Control Female 1	strain:NA\|dev stage:Adult\|sex:female\|tissue:Liver\|genotype:Tg myl7:GAL4 VP16 myl7:cerulean\|BioSampleModel:Model organism or animal	Control Female 1	Illumina 13	Illumina 13	RNA Sample from Liver	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP267510	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	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	India	2020-06-16	Adult	Adult	Liver	Liver and Biliary System
59633	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. 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.		Model organism or animal sample from Danio rerio	IL6 Male 3	strain:NA\|dev stage:Adult\|sex:male\|tissue:Liver\|genotype:Tg myl7:GAL4 VP16 myl7:cerulean::UAS:HsaIL6 myl7:cherry\|BioSampleModel:Model organism or animal	IL6 Male 3	Illumina 11	Illumina 11	RNA Sample from Liver	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP267510	CSL0024_GCCAAT_R1.fastq CSL0024_GCCAAT_R2.fastq	fastq fastq	22675656000.0	75585520.0	CSL0024 GCCAAT R1.fastq	0:150 1:150	A:6117854289;C:5269433434;G:5157725182;T:6126915612;N:3727483	150	150	6117854289	5269433434	5157725182	6126915612	3727483	SRX8555533	SRS6849258	SRA1087578	CSIR-Institute of Genomics and Integrative Biology\|Biological Science	CSIR-Institute of Genomics and Integrative Biology	2	0.92716	0.89411	0.2451	0.22837	0.77893	0.78356	0.49552	0.49248	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	India	2020-06-16	Adult	Adult	Liver	Liver and Biliary System
59634	59634	SRR12023703	SRX8555532	SRS6849257	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.		Model organism or animal sample from Danio rerio	IL6 Male 2	strain:NA\|dev stage:Adult\|sex:male\|tissue:Liver\|genotype:Tg myl7:GAL4 VP16 myl7:cerulean::UAS:HsaIL6 myl7:cherry\|BioSampleModel:Model organism or animal	IL6 Male 2	Illumina 9	Illumina 9	RNA Sample from Liver	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP267510	CSL0023_ACAGTG_R2.fastq CSL0023_ACAGTG_R1.fastq	fastq fastq	13329333900.0	44431113.0	CSL0023 ACAGTG R1.fastq	0:150 1:150	A:3626326258;C:3053126966;G:2977614420;T:3670080924;N:2185332	150	150	3626326258	3053126966	2977614420	3670080924	2185332	SRX8555532	SRS6849257	SRA1087578	CSIR-Institute of Genomics and Integrative Biology\|Biological Science	CSIR-Institute of Genomics and Integrative Biology	2	0.92354	0.88877	0.22391	0.20792	0.78269	0.78875	0.49676	0.49774	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	India	2020-06-16	Adult	Adult	Liver	Liver and Biliary System
59635	59635	SRR12023704	SRX8555531	SRS6849256	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.		Model organism or animal sample from Danio rerio	IL6 Male 1	strain:NA\|dev stage:Adult\|sex:male\|tissue:Liver\|genotype:Tg myl7:GAL4 VP16 myl7:cerulean::UAS:HsaIL6 myl7:cherry\|BioSampleModel:Model organism or animal	IL6 Male 1	Illumina 7	Illumina 7	RNA Sample from Liver	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP267510	CSL0022_TGACCA_R2.fastq CSL0022_TGACCA_R1.fastq	fastq fastq	17822980800.0	59409936.0	CSL0022 TGACCA R1.fastq	0:150 1:150	A:4761067011;C:4172352963;G:4056635108;T:4829992784;N:2932934	150	150	4761067011	4172352963	4056635108	4829992784	2932934	SRX8555531	SRS6849256	SRA1087578	CSIR-Institute of Genomics and Integrative Biology\|Biological Science	CSIR-Institute of Genomics and Integrative Biology	2	0.92357	0.89189	0.1913	0.17898	0.80955	0.81345	0.48272	0.51312	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	India	2020-06-16	Adult	Adult	Liver	Liver and Biliary System
59636	59636	SRR12023705	SRX8555530	SRS6849255	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.		Model organism or animal sample from Danio rerio	Control Male 3	strain:NA\|dev stage:Adult\|sex:male\|tissue:Liver\|genotype:Tg myl7:GAL4 VP16 myl7:cerulean\|BioSampleModel:Model organism or animal	Control Male 3	Illumina 5	Illumina 5	RNA Sample from Liver	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP267510	CSL0021_TTAGGC_R2.fastq CSL0021_TTAGGC_R1.fastq	fastq fastq	11299955100.0	37666517.0	CSL0021 TTAGGC R1.fastq	0:150 1:150	A:3052641657;C:2608127753;G:2567202538;T:3070106887;N:1876265	150	150	3052641657	2608127753	2567202538	3070106887	1876265	SRX8555530	SRS6849255	SRA1087578	CSIR-Institute of Genomics and Integrative Biology\|Biological Science	CSIR-Institute of Genomics and Integrative Biology	2	0.93268	0.89635	0.25559	0.23769	0.80243	0.80697	0.57873	0.58082	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	India	2020-06-16	Adult	Adult	Liver	Liver and Biliary System
59637	59637	SRR12023706	SRX8555529	SRS6849254	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.		Model organism or animal sample from Danio rerio	IL6 Female 3	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	IL6 Female 3	Illumina 23	Illumina 23	RNA Sample from Liver	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP267510	CSL0028_TAGCTT_R1.fastq CSL0028_TAGCTT_R2.fastq	fastq fastq	15892738200.0	52975794.0	CSL0028 TAGCTT R1.fastq	0:150 1:150	A:4055814478;C:3913130542;G:3852912174;T:4069064074;N:1816932	150	150	4055814478	3913130542	3852912174	4069064074	1816932	SRX8555529	SRS6849254	SRA1087578	CSIR-Institute of Genomics and Integrative Biology\|Biological Science	CSIR-Institute of Genomics and Integrative Biology	2	0.93537	0.9116	0.14797	0.13554	0.85472	0.85989	0.28545	0.28363	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	India	2020-06-16	Adult	Adult	Liver	Liver and Biliary System
59638	59638	SRR12023707	SRX8555528	SRS6849253	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.		Model organism or animal sample from Danio rerio	IL6 Female 2	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	IL6 Female 2	Illumina 21	Illumina 21	RNA Sample from Liver	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP267510	CSL0027_GATCAG_R2.fastq CSL0027_GATCAG_R1.fastq	fastq fastq	9571721700.0	31905739.0	CSL0027 GATCAG R1.fastq	0:150 1:150	A:2465870171;C:2344341601;G:2309622279;T:2450779079;N:1108570	150	150	2465870171	2344341601	2309622279	2450779079	1108570	SRX8555528	SRS6849253	SRA1087578	CSIR-Institute of Genomics and Integrative Biology\|Biological Science	CSIR-Institute of Genomics and Integrative Biology	2	0.92386	0.89049	0.19935	0.1825	0.75814	0.76652	0.49177	0.47586	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	India	2020-06-16	Adult	Adult	Liver	Liver and Biliary System
59639	59639	SRR12023708	SRX8555527	SRS6849252	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.		Model organism or animal sample from Danio rerio	Control Male 2	strain:NA\|dev stage:Adult\|sex:male\|tissue:Liver\|genotype:Tg myl7:GAL4 VP16 myl7:cerulean\|BioSampleModel:Model organism or animal	Control Male 2	Illumina 3	Illumina 3	RNA Sample from Liver	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP267510	CSL0020_CGATGT_R1.fastq CSL0020_CGATGT_R2.fastq	fastq fastq	7328390400.0	24427968.0	CSL0020 CGATGT R1.fastq	0:150 1:150	A:1971520921;C:1698238887;G:1662771994;T:1994648164;N:1210434	150	150	1971520921	1698238887	1662771994	1994648164	1210434	SRX8555527	SRS6849252	SRA1087578	CSIR-Institute of Genomics and Integrative Biology\|Biological Science	CSIR-Institute of Genomics and Integrative Biology	2	0.92675	0.89151	0.24309	0.22537	0.79959	0.80614	0.56086	0.57293	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	India	2020-06-16	Adult	Adult	Liver	Liver and Biliary System
59640	59640	SRR12023709	SRX8555526	SRS6849251	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.		Model organism or animal sample from Danio rerio	Control Male 1	strain:NA\|dev stage:Adult\|sex:male\|tissue:Liver\|genotype:Tg myl7:GAL4 VP16 myl7:cerulean\|BioSampleModel:Model organism or animal	Control Male 1	Illumina 1	Illumina 1	RNA Sample from Liver	RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP267510	CSL0019_ATCACG_R2.fastq CSL0019_ATCACG_R1.fastq	fastq fastq	7723873500.0	25746245.0	CSL0019 ATCACG R1.fastq	0:150 1:150	A:2088536483;C:1787588978;G:1733591076;T:2112893078;N:1263885	150	150	2088536483	1787588978	1733591076	2112893078	1263885	SRX8555526	SRS6849251	SRA1087578	CSIR-Institute of Genomics and Integrative Biology\|Biological Science	CSIR-Institute of Genomics and Integrative Biology	2	0.93554	0.90354	0.22565	0.21082	0.80795	0.81298	0.56443	0.56677	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	India	2020-06-16	Adult	Adult	Liver	Liver and Biliary System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;