metadata: run_metadata: 16 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "Oligo-dT" and tissue_curation

16 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "Oligo-dT" and tissue_curation_coarse = "Liver and Biliary System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
77237	77237	SRR25536613	SRX21265881	SRS18518724	SRP451621	PRJNA998935	A new cholesterol diet protocol for zebrafish reveals hypercholesterolemia and fasting associated hepatic steatosis	PRJNA998935	Other	Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid associated disorders. In this study we provide a protocol to assay the impact of a high cholesterol diet HCD on lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB containing lipoproteins ApoB LP and increased plasma levels of cholesterol and cholesterol esters CE. Feeding of the HCD was also associated with a fatty liver phenotype presented as severe hepatic steatosis in zebrafish larvae post feeding the diet for 8 days followed by fasting for 24 hours. Additionally 30 percent of all adult female fish were observed to develop hepatic steatosis post feeding HCD for 2 weeks followed by 3 days of fasting. The HCD feeding paradigm produced elevated levels of liver triacylglycerol TG free cholesterol and CE compared to fish fed the control diet. The doubling of liver TG was striking because our HCD was only supplemented with cholesterol. The accumulated TG in the liver was not likely due to increase de novo lipogenesis or inhibited beta oxidation since we identified no differentially expressed genes in these pathways between the livers of fish fed the HCD and the control diets. However fasted HCD fish had significantly increased expression of the lipogenesis gene fasn in adipose tissue and higher free fatty acids FFA in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes which supplied more FFA during fasting promoting hepatic steatosis. In conclusion our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.	H f LV 3	breed:AB\|dev stage:Adult\|collection date:2021 12 01\|geo loc name:USA: Baltimore\|sex:female\|tissue:Liver\|treatment:4% High cholesterol diet\|Replicate:Biological replicate 3\|BioSampleModel:Model organism or animal	RNAseq of zebrafish liver	H f 17	H f 17	Liver from fish fed either control or high cholesterol diets	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	HCD_Liver_Female_Fish17_S5_L001_R1_001.fastq.gz HCD_Liver_Female_Fish17_S5_L002_R1_001.fastq.gz HCD_Liver_Female_Fish17_S5_L003_R1_001.fastq.gz HCD_Liver_Female_Fish17_S5_L004_R1_001.fastq.gz	fastq fastq fastq fastq	1667981175.0	22239749.0	HCD Liver Female Fish17 S5 L001 R1 001.fastq.gz	0:75	A:425841331;C:377055579;G:401298455;T:463752573;N:33237	75	425841331	377055579	401298455	463752573	33237	SRX21265881	SRS18518724	SRA1687253	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.96371	0.04066	0.84419	0.20092	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2023-08-06	Adult	Adult	Liver	Liver and Biliary System
77238	77238	SRR25536614	SRX21265880	SRS18518723	SRP451621	PRJNA998935	A new cholesterol diet protocol for zebrafish reveals hypercholesterolemia and fasting associated hepatic steatosis	PRJNA998935	Other	Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid associated disorders. In this study we provide a protocol to assay the impact of a high cholesterol diet HCD on lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB containing lipoproteins ApoB LP and increased plasma levels of cholesterol and cholesterol esters CE. Feeding of the HCD was also associated with a fatty liver phenotype presented as severe hepatic steatosis in zebrafish larvae post feeding the diet for 8 days followed by fasting for 24 hours. Additionally 30 percent of all adult female fish were observed to develop hepatic steatosis post feeding HCD for 2 weeks followed by 3 days of fasting. The HCD feeding paradigm produced elevated levels of liver triacylglycerol TG free cholesterol and CE compared to fish fed the control diet. The doubling of liver TG was striking because our HCD was only supplemented with cholesterol. The accumulated TG in the liver was not likely due to increase de novo lipogenesis or inhibited beta oxidation since we identified no differentially expressed genes in these pathways between the livers of fish fed the HCD and the control diets. However fasted HCD fish had significantly increased expression of the lipogenesis gene fasn in adipose tissue and higher free fatty acids FFA in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes which supplied more FFA during fasting promoting hepatic steatosis. In conclusion our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.	C f LV 2	breed:AB\|dev stage:Adult\|collection date:2021 12 01\|geo loc name:USA: Baltimore\|sex:female\|tissue:Liver\|treatment:Control Diet\|Replicate:Biological replicate 2\|BioSampleModel:Model organism or animal	RNAseq of zebrafish liver	C f 11	C f 11	Liver from fish fed either control or high cholesterol diets	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	Control_Liver_Female_Fish11_S7_L001_R1_001.fastq.gz Control_Liver_Female_Fish11_S7_L002_R1_001.fastq.gz Control_Liver_Female_Fish11_S7_L003_R1_001.fastq.gz Control_Liver_Female_Fish11_S7_L004_R1_001.fastq.gz	fastq fastq fastq fastq	2630596725.0	35074623.0	Control Liver Female Fish11 S7 L001 R1 001.fastq.gz	0:75	A:671084571;C:594955811;G:629855406;T:734694929;N:6008	75	671084571	594955811	629855406	734694929	6008	SRX21265880	SRS18518723	SRA1687253	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.9633	0.03018	0.87596	0.2034	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2023-08-06	Adult	Adult	Liver	Liver and Biliary System
77239	77239	SRR25536615	SRX21265879	SRS18518722	SRP451621	PRJNA998935	A new cholesterol diet protocol for zebrafish reveals hypercholesterolemia and fasting associated hepatic steatosis	PRJNA998935	Other	Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid associated disorders. In this study we provide a protocol to assay the impact of a high cholesterol diet HCD on lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB containing lipoproteins ApoB LP and increased plasma levels of cholesterol and cholesterol esters CE. Feeding of the HCD was also associated with a fatty liver phenotype presented as severe hepatic steatosis in zebrafish larvae post feeding the diet for 8 days followed by fasting for 24 hours. Additionally 30 percent of all adult female fish were observed to develop hepatic steatosis post feeding HCD for 2 weeks followed by 3 days of fasting. The HCD feeding paradigm produced elevated levels of liver triacylglycerol TG free cholesterol and CE compared to fish fed the control diet. The doubling of liver TG was striking because our HCD was only supplemented with cholesterol. The accumulated TG in the liver was not likely due to increase de novo lipogenesis or inhibited beta oxidation since we identified no differentially expressed genes in these pathways between the livers of fish fed the HCD and the control diets. However fasted HCD fish had significantly increased expression of the lipogenesis gene fasn in adipose tissue and higher free fatty acids FFA in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes which supplied more FFA during fasting promoting hepatic steatosis. In conclusion our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.	C f LV 1	breed:AB\|dev stage:Adult\|collection date:2021 12 01\|geo loc name:USA: Baltimore\|sex:female\|tissue:Liver\|treatment:Control Diet\|Replicate:Biological replicate 1\|BioSampleModel:Model organism or animal	RNAseq of zebrafish liver	C f 10	C f 10	Liver from fish fed either control or high cholesterol diets	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	Control_Liver_Female_Fish10_S6_L001_R1_001.fastq.gz Control_Liver_Female_Fish10_S6_L002_R1_001.fastq.gz Control_Liver_Female_Fish10_S6_L003_R1_001.fastq.gz Control_Liver_Female_Fish10_S6_L004_R1_001.fastq.gz	fastq fastq fastq fastq	2587110375.0	34494805.0	Control Liver Female Fish10 S6 L001 R1 001.fastq.gz	0:75	A:660359900;C:585827860;G:620545624;T:720371035;N:5956	75	660359900	585827860	620545624	720371035	5956	SRX21265879	SRS18518722	SRA1687253	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.96477	0.03377	0.86738	0.19641	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2023-08-06	Adult	Adult	Liver	Liver and Biliary System
77240	77240	SRR25536616	SRX21265878	SRS18518721	SRP451621	PRJNA998935	A new cholesterol diet protocol for zebrafish reveals hypercholesterolemia and fasting associated hepatic steatosis	PRJNA998935	Other	Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid associated disorders. In this study we provide a protocol to assay the impact of a high cholesterol diet HCD on lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB containing lipoproteins ApoB LP and increased plasma levels of cholesterol and cholesterol esters CE. Feeding of the HCD was also associated with a fatty liver phenotype presented as severe hepatic steatosis in zebrafish larvae post feeding the diet for 8 days followed by fasting for 24 hours. Additionally 30 percent of all adult female fish were observed to develop hepatic steatosis post feeding HCD for 2 weeks followed by 3 days of fasting. The HCD feeding paradigm produced elevated levels of liver triacylglycerol TG free cholesterol and CE compared to fish fed the control diet. The doubling of liver TG was striking because our HCD was only supplemented with cholesterol. The accumulated TG in the liver was not likely due to increase de novo lipogenesis or inhibited beta oxidation since we identified no differentially expressed genes in these pathways between the livers of fish fed the HCD and the control diets. However fasted HCD fish had significantly increased expression of the lipogenesis gene fasn in adipose tissue and higher free fatty acids FFA in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes which supplied more FFA during fasting promoting hepatic steatosis. In conclusion our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.	H f LV 2	breed:AB\|dev stage:Adult\|collection date:2021 12 01\|geo loc name:USA: Baltimore\|sex:female\|tissue:Liver\|treatment:4% High cholesterol diet\|Replicate:Biological replicate 2\|BioSampleModel:Model organism or animal	RNAseq of zebrafish liver	H f 16	H f 16	Liver from fish fed either control or high cholesterol diets	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	HCD_Liver_Female_Fish16_S4_L001_R1_001.fastq.gz HCD_Liver_Female_Fish16_S4_L002_R1_001.fastq.gz HCD_Liver_Female_Fish16_S4_L003_R1_001.fastq.gz HCD_Liver_Female_Fish16_S4_L004_R1_001.fastq.gz	fastq fastq fastq fastq	2310746250.0	30809950.0	HCD Liver Female Fish16 S4 L001 R1 001.fastq.gz	0:75	A:585197224;C:522895915;G:554709931;T:647898858;N:44322	75	585197224	522895915	554709931	647898858	44322	SRX21265878	SRS18518721	SRA1687253	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.96111	0.03948	0.86724	0.24235	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2023-08-06	Adult	Adult	Liver	Liver and Biliary System
77241	77241	SRR25536617	SRX21265877	SRS18518720	SRP451621	PRJNA998935	A new cholesterol diet protocol for zebrafish reveals hypercholesterolemia and fasting associated hepatic steatosis	PRJNA998935	Other	Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid associated disorders. In this study we provide a protocol to assay the impact of a high cholesterol diet HCD on lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB containing lipoproteins ApoB LP and increased plasma levels of cholesterol and cholesterol esters CE. Feeding of the HCD was also associated with a fatty liver phenotype presented as severe hepatic steatosis in zebrafish larvae post feeding the diet for 8 days followed by fasting for 24 hours. Additionally 30 percent of all adult female fish were observed to develop hepatic steatosis post feeding HCD for 2 weeks followed by 3 days of fasting. The HCD feeding paradigm produced elevated levels of liver triacylglycerol TG free cholesterol and CE compared to fish fed the control diet. The doubling of liver TG was striking because our HCD was only supplemented with cholesterol. The accumulated TG in the liver was not likely due to increase de novo lipogenesis or inhibited beta oxidation since we identified no differentially expressed genes in these pathways between the livers of fish fed the HCD and the control diets. However fasted HCD fish had significantly increased expression of the lipogenesis gene fasn in adipose tissue and higher free fatty acids FFA in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes which supplied more FFA during fasting promoting hepatic steatosis. In conclusion our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.	H f LV 1	breed:AB\|dev stage:Adult\|collection date:2021 12 01\|geo loc name:USA: Baltimore\|sex:female\|tissue:Liver\|treatment:4% High cholesterol diet\|Replicate:Biological replicate 1\|BioSampleModel:Model organism or animal	RNAseq of zebrafish liver	H f 13	H f 13	Liver from fish fed either control or high cholesterol diets	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	HCD_Liver_Female_Fish13_S3_L001_R1_001.fastq.gz HCD_Liver_Female_Fish13_S3_L002_R1_001.fastq.gz HCD_Liver_Female_Fish13_S3_L003_R1_001.fastq.gz HCD_Liver_Female_Fish13_S3_L004_R1_001.fastq.gz	fastq fastq fastq fastq	2252189250.0	30029190.0	HCD Liver Female Fish13 S3 L001 R1 001.fastq.gz	0:75	A:570971767;C:509747304;G:535901310;T:635524543;N:44326	75	570971767	509747304	535901310	635524543	44326	SRX21265877	SRS18518720	SRA1687253	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.96187	0.04018	0.86823	0.28843	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2023-08-06	Adult	Adult	Liver	Liver and Biliary System
77242	77242	SRR25536618	SRX21265876	SRS18518719	SRP451621	PRJNA998935	A new cholesterol diet protocol for zebrafish reveals hypercholesterolemia and fasting associated hepatic steatosis	PRJNA998935	Other	Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid associated disorders. In this study we provide a protocol to assay the impact of a high cholesterol diet HCD on lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB containing lipoproteins ApoB LP and increased plasma levels of cholesterol and cholesterol esters CE. Feeding of the HCD was also associated with a fatty liver phenotype presented as severe hepatic steatosis in zebrafish larvae post feeding the diet for 8 days followed by fasting for 24 hours. Additionally 30 percent of all adult female fish were observed to develop hepatic steatosis post feeding HCD for 2 weeks followed by 3 days of fasting. The HCD feeding paradigm produced elevated levels of liver triacylglycerol TG free cholesterol and CE compared to fish fed the control diet. The doubling of liver TG was striking because our HCD was only supplemented with cholesterol. The accumulated TG in the liver was not likely due to increase de novo lipogenesis or inhibited beta oxidation since we identified no differentially expressed genes in these pathways between the livers of fish fed the HCD and the control diets. However fasted HCD fish had significantly increased expression of the lipogenesis gene fasn in adipose tissue and higher free fatty acids FFA in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes which supplied more FFA during fasting promoting hepatic steatosis. In conclusion our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.	C m LV 4	breed:AB\|dev stage:Adult\|collection date:2021 12 01\|geo loc name:USA: Baltimore\|sex:male\|tissue:Liver\|treatment:Control Diet\|Replicate:Biological replicate 4\|BioSampleModel:Model organism or animal	RNAseq of zebrafish liver	C m 22	C m 22	Liver from fish fed either control or high cholesterol diets	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	Control_Liver_Male_Fish22_S2_L001_R1_001.fastq.gz Control_Liver_Male_Fish22_S2_L002_R1_001.fastq.gz Control_Liver_Male_Fish22_S2_L003_R1_001.fastq.gz Control_Liver_Male_Fish22_S2_L004_R1_001.fastq.gz	fastq fastq fastq fastq	3576644025.0	47688587.0	Control Liver Male Fish22 S2 L001 R1 001.fastq.gz	0:75	A:901502654;C:798874087;G:851325162;T:1024872444;N:69678	75	901502654	798874087	851325162	1024872444	69678	SRX21265876	SRS18518719	SRA1687253	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.94197	0.05999	0.82777	0.50866	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2023-08-06	Adult	Adult	Liver	Liver and Biliary System
77243	77243	SRR25536619	SRX21265875	SRS18518718	SRP451621	PRJNA998935	A new cholesterol diet protocol for zebrafish reveals hypercholesterolemia and fasting associated hepatic steatosis	PRJNA998935	Other	Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid associated disorders. In this study we provide a protocol to assay the impact of a high cholesterol diet HCD on lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB containing lipoproteins ApoB LP and increased plasma levels of cholesterol and cholesterol esters CE. Feeding of the HCD was also associated with a fatty liver phenotype presented as severe hepatic steatosis in zebrafish larvae post feeding the diet for 8 days followed by fasting for 24 hours. Additionally 30 percent of all adult female fish were observed to develop hepatic steatosis post feeding HCD for 2 weeks followed by 3 days of fasting. The HCD feeding paradigm produced elevated levels of liver triacylglycerol TG free cholesterol and CE compared to fish fed the control diet. The doubling of liver TG was striking because our HCD was only supplemented with cholesterol. The accumulated TG in the liver was not likely due to increase de novo lipogenesis or inhibited beta oxidation since we identified no differentially expressed genes in these pathways between the livers of fish fed the HCD and the control diets. However fasted HCD fish had significantly increased expression of the lipogenesis gene fasn in adipose tissue and higher free fatty acids FFA in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes which supplied more FFA during fasting promoting hepatic steatosis. In conclusion our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.	C m LV 3	breed:AB\|dev stage:Adult\|collection date:2021 12 01\|geo loc name:USA: Baltimore\|sex:male\|tissue:Liver\|treatment:Control Diet\|Replicate:Biological replicate 3\|BioSampleModel:Model organism or animal	RNAseq of zebrafish liver	C m 20	C m 20	Liver from fish fed either control or high cholesterol diets	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	Control_Liver_Male_Fish20_S1_L001_R1_001.fastq.gz Control_Liver_Male_Fish20_S1_L002_R1_001.fastq.gz Control_Liver_Male_Fish20_S1_L003_R1_001.fastq.gz Control_Liver_Male_Fish20_S1_L004_R1_001.fastq.gz	fastq fastq fastq fastq	3516477150.0	46886362.0	Control Liver Male Fish20 S1 L001 R1 001.fastq.gz	0:75	A:881536366;C:786657878;G:831133599;T:1017082181;N:67126	75	881536366	786657878	831133599	1017082181	67126	SRX21265875	SRS18518718	SRA1687253	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.93731	0.06298	0.81257	0.55948	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2023-08-06	Adult	Adult	Liver	Liver and Biliary System
77244	77244	SRR25536620	SRX21265874	SRS18518717	SRP451621	PRJNA998935	A new cholesterol diet protocol for zebrafish reveals hypercholesterolemia and fasting associated hepatic steatosis	PRJNA998935	Other	Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid associated disorders. In this study we provide a protocol to assay the impact of a high cholesterol diet HCD on lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB containing lipoproteins ApoB LP and increased plasma levels of cholesterol and cholesterol esters CE. Feeding of the HCD was also associated with a fatty liver phenotype presented as severe hepatic steatosis in zebrafish larvae post feeding the diet for 8 days followed by fasting for 24 hours. Additionally 30 percent of all adult female fish were observed to develop hepatic steatosis post feeding HCD for 2 weeks followed by 3 days of fasting. The HCD feeding paradigm produced elevated levels of liver triacylglycerol TG free cholesterol and CE compared to fish fed the control diet. The doubling of liver TG was striking because our HCD was only supplemented with cholesterol. The accumulated TG in the liver was not likely due to increase de novo lipogenesis or inhibited beta oxidation since we identified no differentially expressed genes in these pathways between the livers of fish fed the HCD and the control diets. However fasted HCD fish had significantly increased expression of the lipogenesis gene fasn in adipose tissue and higher free fatty acids FFA in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes which supplied more FFA during fasting promoting hepatic steatosis. In conclusion our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.	C m LV 2	breed:AB\|dev stage:Adult\|collection date:2021 12 01\|geo loc name:USA: Baltimore\|sex:male\|tissue:Liver\|treatment:Control Diet\|Replicate:Biological replicate 2\|BioSampleModel:Model organism or animal	RNAseq of zebrafish liver	C m 19	C m 19	Liver from fish fed either control or high cholesterol diets	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	Control_Liver_Male_Fish19_S17_L001_R1_001.fastq.gz Control_Liver_Male_Fish19_S17_L002_R1_001.fastq.gz Control_Liver_Male_Fish19_S17_L003_R1_001.fastq.gz Control_Liver_Male_Fish19_S17_L004_R1_001.fastq.gz	fastq fastq fastq fastq	1305613875.0	17408185.0	Control Liver Male Fish19 S17 L001 R1 001.fastq.gz	0:75	A:331036688;C:294175998;G:305542007;T:374856319;N:2863	75	331036688	294175998	305542007	374856319	2863	SRX21265874	SRS18518717	SRA1687253	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.93476	0.06942	0.80706	0.57415	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2023-08-06	Adult	Adult	Liver	Liver and Biliary System
77245	77245	SRR25536621	SRX21265873	SRS18518716	SRP451621	PRJNA998935	A new cholesterol diet protocol for zebrafish reveals hypercholesterolemia and fasting associated hepatic steatosis	PRJNA998935	Other	Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid associated disorders. In this study we provide a protocol to assay the impact of a high cholesterol diet HCD on lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB containing lipoproteins ApoB LP and increased plasma levels of cholesterol and cholesterol esters CE. Feeding of the HCD was also associated with a fatty liver phenotype presented as severe hepatic steatosis in zebrafish larvae post feeding the diet for 8 days followed by fasting for 24 hours. Additionally 30 percent of all adult female fish were observed to develop hepatic steatosis post feeding HCD for 2 weeks followed by 3 days of fasting. The HCD feeding paradigm produced elevated levels of liver triacylglycerol TG free cholesterol and CE compared to fish fed the control diet. The doubling of liver TG was striking because our HCD was only supplemented with cholesterol. The accumulated TG in the liver was not likely due to increase de novo lipogenesis or inhibited beta oxidation since we identified no differentially expressed genes in these pathways between the livers of fish fed the HCD and the control diets. However fasted HCD fish had significantly increased expression of the lipogenesis gene fasn in adipose tissue and higher free fatty acids FFA in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes which supplied more FFA during fasting promoting hepatic steatosis. In conclusion our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.	C m LV 1	breed:AB\|dev stage:Adult\|collection date:2021 12 01\|geo loc name:USA: Baltimore\|sex:male\|tissue:Liver\|treatment:Control Diet\|Replicate:Biological replicate 1\|BioSampleModel:Model organism or animal	RNAseq of zebrafish liver	C m 13	C m 13	Liver from fish fed either control or high cholesterol diets	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	Control_Liver_Male_Fish13_S14_L001_R1_001.fastq.gz Control_Liver_Male_Fish13_S14_L002_R1_001.fastq.gz Control_Liver_Male_Fish13_S14_L003_R1_001.fastq.gz Control_Liver_Male_Fish13_S14_L004_R1_001.fastq.gz	fastq fastq fastq fastq	1268532450.0	16913766.0	Control Liver Male Fish13 S14 L001 R1 001.fastq.gz	0:75	A:322874272;C:283845058;G:297472388;T:364338049;N:2683	75	322874272	283845058	297472388	364338049	2683	SRX21265873	SRS18518716	SRA1687253	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.93379	0.06633	0.83037	0.58242	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2023-08-06	Adult	Adult	Liver	Liver and Biliary System
77246	77246	SRR25536622	SRX21265872	SRS18518715	SRP451621	PRJNA998935	A new cholesterol diet protocol for zebrafish reveals hypercholesterolemia and fasting associated hepatic steatosis	PRJNA998935	Other	Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid associated disorders. In this study we provide a protocol to assay the impact of a high cholesterol diet HCD on lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB containing lipoproteins ApoB LP and increased plasma levels of cholesterol and cholesterol esters CE. Feeding of the HCD was also associated with a fatty liver phenotype presented as severe hepatic steatosis in zebrafish larvae post feeding the diet for 8 days followed by fasting for 24 hours. Additionally 30 percent of all adult female fish were observed to develop hepatic steatosis post feeding HCD for 2 weeks followed by 3 days of fasting. The HCD feeding paradigm produced elevated levels of liver triacylglycerol TG free cholesterol and CE compared to fish fed the control diet. The doubling of liver TG was striking because our HCD was only supplemented with cholesterol. The accumulated TG in the liver was not likely due to increase de novo lipogenesis or inhibited beta oxidation since we identified no differentially expressed genes in these pathways between the livers of fish fed the HCD and the control diets. However fasted HCD fish had significantly increased expression of the lipogenesis gene fasn in adipose tissue and higher free fatty acids FFA in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes which supplied more FFA during fasting promoting hepatic steatosis. In conclusion our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.	C f LV 4	breed:AB\|dev stage:Adult\|collection date:2021 12 01\|geo loc name:USA: Baltimore\|sex:female\|tissue:Liver\|treatment:Control Diet\|Replicate:Biological replicate 4\|BioSampleModel:Model organism or animal	RNAseq of zebrafish liver	C f 17	C f 17	Liver from fish fed either control or high cholesterol diets	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	Control_Liver_Female_Fish17_S16_L001_R1_001.fastq.gz Control_Liver_Female_Fish17_S16_L002_R1_001.fastq.gz Control_Liver_Female_Fish17_S16_L003_R1_001.fastq.gz Control_Liver_Female_Fish17_S16_L004_R1_001.fastq.gz	fastq fastq fastq fastq	1179181575.0	15722421.0	Control Liver Female Fish17 S16 L001 R1 001.fastq.gz	0:75	A:301365228;C:268629404;G:280805128;T:328379299;N:2516	75	301365228	268629404	280805128	328379299	2516	SRX21265872	SRS18518715	SRA1687253	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.96625	0.03131	0.89059	0.21165	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2023-08-06	Adult	Adult	Liver	Liver and Biliary System
77247	77247	SRR25536623	SRX21265871	SRS18518714	SRP451621	PRJNA998935	A new cholesterol diet protocol for zebrafish reveals hypercholesterolemia and fasting associated hepatic steatosis	PRJNA998935	Other	Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid associated disorders. In this study we provide a protocol to assay the impact of a high cholesterol diet HCD on lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB containing lipoproteins ApoB LP and increased plasma levels of cholesterol and cholesterol esters CE. Feeding of the HCD was also associated with a fatty liver phenotype presented as severe hepatic steatosis in zebrafish larvae post feeding the diet for 8 days followed by fasting for 24 hours. Additionally 30 percent of all adult female fish were observed to develop hepatic steatosis post feeding HCD for 2 weeks followed by 3 days of fasting. The HCD feeding paradigm produced elevated levels of liver triacylglycerol TG free cholesterol and CE compared to fish fed the control diet. The doubling of liver TG was striking because our HCD was only supplemented with cholesterol. The accumulated TG in the liver was not likely due to increase de novo lipogenesis or inhibited beta oxidation since we identified no differentially expressed genes in these pathways between the livers of fish fed the HCD and the control diets. However fasted HCD fish had significantly increased expression of the lipogenesis gene fasn in adipose tissue and higher free fatty acids FFA in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes which supplied more FFA during fasting promoting hepatic steatosis. In conclusion our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.	C f LV 3	breed:AB\|dev stage:Adult\|collection date:2021 12 01\|geo loc name:USA: Baltimore\|sex:female\|tissue:Liver\|treatment:Control Diet\|Replicate:Biological replicate 3\|BioSampleModel:Model organism or animal	RNAseq of zebrafish liver	C f 14	C f 14	Liver from fish fed either control or high cholesterol diets	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	Control_Liver_Female_Fish14_S15_L001_R1_001.fastq.gz Control_Liver_Female_Fish14_S15_L002_R1_001.fastq.gz Control_Liver_Female_Fish14_S15_L003_R1_001.fastq.gz Control_Liver_Female_Fish14_S15_L004_R1_001.fastq.gz	fastq fastq fastq fastq	1026856125.0	13691415.0	Control Liver Female Fish14 S15 L001 R1 001.fastq.gz	0:75	A:258693442;C:234865725;G:244672557;T:288622155;N:2246	75	258693442	234865725	244672557	288622155	2246	SRX21265871	SRS18518714	SRA1687253	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.95687	0.04113	0.85587	0.34357	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2023-08-06	Adult	Adult	Liver	Liver and Biliary System
77248	77248	SRR25536624	SRX21265870	SRS18518713	SRP451621	PRJNA998935	A new cholesterol diet protocol for zebrafish reveals hypercholesterolemia and fasting associated hepatic steatosis	PRJNA998935	Other	Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid associated disorders. In this study we provide a protocol to assay the impact of a high cholesterol diet HCD on lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB containing lipoproteins ApoB LP and increased plasma levels of cholesterol and cholesterol esters CE. Feeding of the HCD was also associated with a fatty liver phenotype presented as severe hepatic steatosis in zebrafish larvae post feeding the diet for 8 days followed by fasting for 24 hours. Additionally 30 percent of all adult female fish were observed to develop hepatic steatosis post feeding HCD for 2 weeks followed by 3 days of fasting. The HCD feeding paradigm produced elevated levels of liver triacylglycerol TG free cholesterol and CE compared to fish fed the control diet. The doubling of liver TG was striking because our HCD was only supplemented with cholesterol. The accumulated TG in the liver was not likely due to increase de novo lipogenesis or inhibited beta oxidation since we identified no differentially expressed genes in these pathways between the livers of fish fed the HCD and the control diets. However fasted HCD fish had significantly increased expression of the lipogenesis gene fasn in adipose tissue and higher free fatty acids FFA in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes which supplied more FFA during fasting promoting hepatic steatosis. In conclusion our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.	H m LV 4	breed:AB\|dev stage:Adult\|collection date:2021 12 01\|geo loc name:USA: Baltimore\|sex:male\|tissue:Liver\|treatment:4% High cholesterol diet\|Replicate:Biological replicate 4\|BioSampleModel:Model organism or animal	RNAseq of zebrafish liver	H m 23	H m 23	Liver from fish fed either control or high cholesterol diets	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	HCD_Liver_Male_Fish223_S10_L001_R1_001.fastq.gz HCD_Liver_Male_Fish223_S10_L002_R1_001.fastq.gz HCD_Liver_Male_Fish223_S10_L003_R1_001.fastq.gz HCD_Liver_Male_Fish223_S10_L004_R1_001.fastq.gz	fastq fastq fastq fastq	2218153050.0	29575374.0	HCD Liver Male Fish223 S10 L001 R1 001.fastq.gz	0:75	A:559011964;C:491371080;G:524026845;T:643700647;N:42514	75	559011964	491371080	524026845	643700647	42514	SRX21265870	SRS18518713	SRA1687253	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.93229	0.06971	0.82483	0.57627	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2023-08-06	Adult	Adult	Liver	Liver and Biliary System
77249	77249	SRR25536625	SRX21265869	SRS18518712	SRP451621	PRJNA998935	A new cholesterol diet protocol for zebrafish reveals hypercholesterolemia and fasting associated hepatic steatosis	PRJNA998935	Other	Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid associated disorders. In this study we provide a protocol to assay the impact of a high cholesterol diet HCD on lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB containing lipoproteins ApoB LP and increased plasma levels of cholesterol and cholesterol esters CE. Feeding of the HCD was also associated with a fatty liver phenotype presented as severe hepatic steatosis in zebrafish larvae post feeding the diet for 8 days followed by fasting for 24 hours. Additionally 30 percent of all adult female fish were observed to develop hepatic steatosis post feeding HCD for 2 weeks followed by 3 days of fasting. The HCD feeding paradigm produced elevated levels of liver triacylglycerol TG free cholesterol and CE compared to fish fed the control diet. The doubling of liver TG was striking because our HCD was only supplemented with cholesterol. The accumulated TG in the liver was not likely due to increase de novo lipogenesis or inhibited beta oxidation since we identified no differentially expressed genes in these pathways between the livers of fish fed the HCD and the control diets. However fasted HCD fish had significantly increased expression of the lipogenesis gene fasn in adipose tissue and higher free fatty acids FFA in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes which supplied more FFA during fasting promoting hepatic steatosis. In conclusion our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.	H m LV 3	breed:AB\|dev stage:Adult\|collection date:2021 12 01\|geo loc name:USA: Baltimore\|sex:male\|tissue:Liver\|treatment:4% High cholesterol diet\|Replicate:Biological replicate 3\|BioSampleModel:Model organism or animal	RNAseq of zebrafish liver	H m 22	H m 22	Liver from fish fed either control or high cholesterol diets	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	HCD_Liver_Male_Fish22_S9_L001_R1_001.fastq.gz HCD_Liver_Male_Fish22_S9_L002_R1_001.fastq.gz HCD_Liver_Male_Fish22_S9_L003_R1_001.fastq.gz HCD_Liver_Male_Fish22_S9_L004_R1_001.fastq.gz	fastq fastq fastq fastq	2636194125.0	35149255.0	HCD Liver Male Fish22 S9 L001 R1 001.fastq.gz	0:75	A:661291859;C:585816263;G:622887679;T:766147545;N:50779	75	661291859	585816263	622887679	766147545	50779	SRX21265869	SRS18518712	SRA1687253	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.93083	0.0675	0.82724	0.58243	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2023-08-06	Adult	Adult	Liver	Liver and Biliary System
77250	77250	SRR25536626	SRX21265868	SRS18518711	SRP451621	PRJNA998935	A new cholesterol diet protocol for zebrafish reveals hypercholesterolemia and fasting associated hepatic steatosis	PRJNA998935	Other	Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid associated disorders. In this study we provide a protocol to assay the impact of a high cholesterol diet HCD on lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB containing lipoproteins ApoB LP and increased plasma levels of cholesterol and cholesterol esters CE. Feeding of the HCD was also associated with a fatty liver phenotype presented as severe hepatic steatosis in zebrafish larvae post feeding the diet for 8 days followed by fasting for 24 hours. Additionally 30 percent of all adult female fish were observed to develop hepatic steatosis post feeding HCD for 2 weeks followed by 3 days of fasting. The HCD feeding paradigm produced elevated levels of liver triacylglycerol TG free cholesterol and CE compared to fish fed the control diet. The doubling of liver TG was striking because our HCD was only supplemented with cholesterol. The accumulated TG in the liver was not likely due to increase de novo lipogenesis or inhibited beta oxidation since we identified no differentially expressed genes in these pathways between the livers of fish fed the HCD and the control diets. However fasted HCD fish had significantly increased expression of the lipogenesis gene fasn in adipose tissue and higher free fatty acids FFA in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes which supplied more FFA during fasting promoting hepatic steatosis. In conclusion our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.	H m LV 2	breed:AB\|dev stage:Adult\|collection date:2021 12 01\|geo loc name:USA: Baltimore\|sex:male\|tissue:Liver\|treatment:4% High cholesterol diet\|Replicate:Biological replicate 2\|BioSampleModel:Model organism or animal	RNAseq of zebrafish liver	H m 21	H m 21	Liver from fish fed either control or high cholesterol diets	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	HCD_Liver_Male_Fish21_S8_L001_R1_001.fastq.gz HCD_Liver_Male_Fish21_S8_L002_R1_001.fastq.gz HCD_Liver_Male_Fish21_S8_L003_R1_001.fastq.gz HCD_Liver_Male_Fish21_S8_L004_R1_001.fastq.gz	fastq fastq fastq fastq	1692392550.0	22565234.0	HCD Liver Male Fish21 S8 L001 R1 001.fastq.gz	0:75	A:428590180;C:371248521;G:399529736;T:492990799;N:33314	75	428590180	371248521	399529736	492990799	33314	SRX21265868	SRS18518711	SRA1687253	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.93669	0.06452	0.83489	0.5964	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2023-08-06	Adult	Adult	Liver	Liver and Biliary System
77251	77251	SRR25536627	SRX21265867	SRS18518710	SRP451621	PRJNA998935	A new cholesterol diet protocol for zebrafish reveals hypercholesterolemia and fasting associated hepatic steatosis	PRJNA998935	Other	Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid associated disorders. In this study we provide a protocol to assay the impact of a high cholesterol diet HCD on lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB containing lipoproteins ApoB LP and increased plasma levels of cholesterol and cholesterol esters CE. Feeding of the HCD was also associated with a fatty liver phenotype presented as severe hepatic steatosis in zebrafish larvae post feeding the diet for 8 days followed by fasting for 24 hours. Additionally 30 percent of all adult female fish were observed to develop hepatic steatosis post feeding HCD for 2 weeks followed by 3 days of fasting. The HCD feeding paradigm produced elevated levels of liver triacylglycerol TG free cholesterol and CE compared to fish fed the control diet. The doubling of liver TG was striking because our HCD was only supplemented with cholesterol. The accumulated TG in the liver was not likely due to increase de novo lipogenesis or inhibited beta oxidation since we identified no differentially expressed genes in these pathways between the livers of fish fed the HCD and the control diets. However fasted HCD fish had significantly increased expression of the lipogenesis gene fasn in adipose tissue and higher free fatty acids FFA in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes which supplied more FFA during fasting promoting hepatic steatosis. In conclusion our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.	H m LV 1	breed:AB\|dev stage:Adult\|collection date:2021 12 01\|geo loc name:USA: Baltimore\|sex:male\|tissue:Liver\|treatment:4% High cholesterol diet\|Replicate:Biological replicate 1\|BioSampleModel:Model organism or animal	RNAseq of zebrafish liver	H m 20	H m 20	Liver from fish fed either control or high cholesterol diets	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	HCD_Liver_Male_Fish20_S7_L001_R1_001.fastq.gz HCD_Liver_Male_Fish20_S7_L002_R1_001.fastq.gz HCD_Liver_Male_Fish20_S7_L003_R1_001.fastq.gz HCD_Liver_Male_Fish20_S7_L004_R1_001.fastq.gz	fastq fastq fastq fastq	1764087525.0	23521167.0	HCD Liver Male Fish20 S7 L001 R1 001.fastq.gz	0:75	A:443743093;C:391319913;G:418728066;T:510263736;N:32717	75	443743093	391319913	418728066	510263736	32717	SRX21265867	SRS18518710	SRA1687253	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.93531	0.06924	0.82562	0.57605	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2023-08-06	Adult	Adult	Liver	Liver and Biliary System
77252	77252	SRR25536628	SRX21265866	SRS18518709	SRP451621	PRJNA998935	A new cholesterol diet protocol for zebrafish reveals hypercholesterolemia and fasting associated hepatic steatosis	PRJNA998935	Other	Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid associated disorders. In this study we provide a protocol to assay the impact of a high cholesterol diet HCD on lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB containing lipoproteins ApoB LP and increased plasma levels of cholesterol and cholesterol esters CE. Feeding of the HCD was also associated with a fatty liver phenotype presented as severe hepatic steatosis in zebrafish larvae post feeding the diet for 8 days followed by fasting for 24 hours. Additionally 30 percent of all adult female fish were observed to develop hepatic steatosis post feeding HCD for 2 weeks followed by 3 days of fasting. The HCD feeding paradigm produced elevated levels of liver triacylglycerol TG free cholesterol and CE compared to fish fed the control diet. The doubling of liver TG was striking because our HCD was only supplemented with cholesterol. The accumulated TG in the liver was not likely due to increase de novo lipogenesis or inhibited beta oxidation since we identified no differentially expressed genes in these pathways between the livers of fish fed the HCD and the control diets. However fasted HCD fish had significantly increased expression of the lipogenesis gene fasn in adipose tissue and higher free fatty acids FFA in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes which supplied more FFA during fasting promoting hepatic steatosis. In conclusion our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.	H f LV 4	breed:AB\|dev stage:Adult\|collection date:2021 12 01\|geo loc name:USA: Baltimore\|sex:female\|tissue:Liver\|treatment:4% High cholesterol diet\|Replicate:Biological replicate 4\|BioSampleModel:Model organism or animal	RNAseq of zebrafish liver	H f 18	H f 18	Liver from fish fed either control or high cholesterol diets	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	HCD_Liver_Female_Fish18_S6_L001_R1_001.fastq.gz HCD_Liver_Female_Fish18_S6_L002_R1_001.fastq.gz HCD_Liver_Female_Fish18_S6_L003_R1_001.fastq.gz HCD_Liver_Female_Fish18_S6_L004_R1_001.fastq.gz	fastq fastq fastq fastq	1575873000.0	21011640.0	HCD Liver Female Fish18 S6 L001 R1 001.fastq.gz	0:75	A:391987980;C:360283535;G:379540225;T:444031680;N:29580	75	391987980	360283535	379540225	444031680	29580	SRX21265866	SRS18518709	SRA1687253	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.95702	0.04341	0.85038	0.37716	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2023-08-06	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");;