metadata: run_metadata: 8 rows where experiment.library_selection = "Oligo-dT", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation

8 rows where experiment.library_selection = "Oligo-dT", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation_coarse = "Adipose Tissue"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	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.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
77253	77253	SRR25432801	SRX21167056	SRS18428841	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.	Adipose tissue 4% HCD diet Fish 4	H 5 Adipose	strain:AB\|age:Adult\|collection date:2022 11 18\|geo loc name:USA: Baltimore\|sex:female\|tissue:Adipose\|treatment:4% high cholesterol diet\|Replicate:Fish 4\|BioSampleModel:Model organism or animal	Adipose tissue 4% HCD diet Fish 4	H 5 Adipose	H 5 Adipose	Total RNA was extracted using Direct zol RNA Microprep Kits R2061 Zymo Research Irvine CA USA. Library was prepared using TruSeq Stranded mRNA Library Prep Kit Illumina San Diego USA	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	H_5_Adipose_S13_L001_R1_001.fastq.gz H_5_Adipose_S13_L002_R1_001.fastq.gz H_5_Adipose_S13_L003_R1_001.fastq.gz H_5_Adipose_S13_L004_R1_001.fastq.gz	fastq fastq fastq fastq	2451969450.0	32692926.0	H 5 Adipose S13 L001 R1 001.fastq.gz	0:75	A:594449440;C:603429442;G:613467936;T:640525800;N:96832	75	594449440	603429442	613467936	640525800	96832	SRX21167056	SRS18428841	SRA1681062	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.9497	0.02663	0.75132	0.50461	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-26	Adult	Adult	Adipose Tissue	Adipose Tissue
77254	77254	SRR25432802	SRX21167055	SRS18428838	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.	Adipose tissue 4% HCD diet Fish 3	H 4 Adipose	strain:AB\|age:Adult\|collection date:2022 11 18\|geo loc name:USA: Baltimore\|sex:female\|tissue:Adipose\|treatment:4% high cholesterol diet\|Replicate:Fish 3\|BioSampleModel:Model organism or animal	Adipose tissue 4% HCD diet Fish 3	H 4 Adipose	H 4 Adipose	Total RNA was extracted using Direct zol RNA Microprep Kits R2061 Zymo Research Irvine CA USA. Library was prepared using TruSeq Stranded mRNA Library Prep Kit Illumina San Diego USA	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	H_4_Adipose_S12_L004_R1_001.fastq.gz H_4_Adipose_S12_L003_R1_001.fastq.gz H_4_Adipose_S12_L002_R1_001.fastq.gz H_4_Adipose_S12_L001_R1_001.fastq.gz	fastq fastq fastq fastq	2726199375.0	36349325.0	H 4 Adipose S12 L001 R1 001.fastq.gz	0:75	A:656159453;C:668829553;G:683259767;T:717842852;N:107750	75	656159453	668829553	683259767	717842852	107750	SRX21167055	SRS18428838	SRA1681062	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.94692	0.01408	0.76406	0.46793	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-26	Adult	Adult	Adipose Tissue	Adipose Tissue
77255	77255	SRR25432803	SRX21167054	SRS18428839	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.	Adipose tissue 4% HCD diet Fish 2	H 3 Adipose	strain:AB\|age:Adult\|collection date:2022 11 18\|geo loc name:USA: Baltimore\|sex:female\|tissue:Adipose\|treatment:4% high cholesterol diet\|Replicate:Fish 2\|BioSampleModel:Model organism or animal	Adipose tissue 4% HCD diet Fish 2	H 3 Adipose	H 3 Adipose	Total RNA was extracted using Direct zol RNA Microprep Kits R2061 Zymo Research Irvine CA USA. Library was prepared using TruSeq Stranded mRNA Library Prep Kit Illumina San Diego USA	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	H_3_Adipose_S10_L001_R1_001.fastq.gz H_3_Adipose_S10_L002_R1_001.fastq.gz H_3_Adipose_S10_L003_R1_001.fastq.gz H_3_Adipose_S10_L004_R1_001.fastq.gz	fastq fastq fastq fastq	2688606825.0	35848091.0	H 3 Adipose S10 L001 R1 001.fastq.gz	0:75	A:660810190;C:640144473;G:665399868;T:722147848;N:104446	75	660810190	640144473	665399868	722147848	104446	SRX21167054	SRS18428839	SRA1681062	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.9536	0.03224	0.73361	0.45126	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-26	Adult	Adult	Adipose Tissue	Adipose Tissue
77256	77256	SRR25432804	SRX21167053	SRS18428840	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.	Adipose tissue 4% HCD diet Fish 1	H 2 Adipose	strain:AB\|age:Adult\|collection date:2022 11 18\|geo loc name:USA: Baltimore\|sex:female\|tissue:Adipose\|treatment:4% high cholesterol diet\|Replicate:Fish 1\|BioSampleModel:Model organism or animal	Adipose tissue 4% HCD diet Fish 1	H 2 Adipose	H 2 Adipose	Total RNA was extracted using Direct zol RNA Microprep Kits R2061 Zymo Research Irvine CA USA. Library was prepared using TruSeq Stranded mRNA Library Prep Kit Illumina San Diego USA	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	H_2_Adipose_S9_L004_R1_001.fastq.gz H_2_Adipose_S9_L003_R1_001.fastq.gz H_2_Adipose_S9_L002_R1_001.fastq.gz H_2_Adipose_S9_L001_R1_001.fastq.gz	fastq fastq fastq fastq	2498108625.0	33308115.0	H 2 Adipose S9 L001 R1 001.fastq.gz	0:75	A:636972494;C:580511829;G:604198966;T:676328320;N:97016	75	636972494	580511829	604198966	676328320	97016	SRX21167053	SRS18428840	SRA1681062	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.94491	0.06922	0.75726	0.5635	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-26	Adult	Adult	Adipose Tissue	Adipose Tissue
77257	77257	SRR25432805	SRX21167052	SRS18428837	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.	Adipose tissue Control diet Fish 4	C 5 Adipose	strain:AB\|age:Adult\|collection date:2022 11 18\|geo loc name:USA: Baltimore\|sex:female\|tissue:Adipose\|treatment:Control diet\|Replicate:Fish 4\|BioSampleModel:Model organism or animal	Adipose tissue Control diet Fish 4	C 5 Adipose	C 5 Adipose	Total RNA was extracted using Direct zol RNA Microprep Kits R2061 Zymo Research Irvine CA USA. Library was prepared using TruSeq Stranded mRNA Library Prep Kit Illumina San Diego USA	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	C_5_Adipose_S7_L001_R1_001.fastq.gz C_5_Adipose_S7_L002_R1_001.fastq.gz C_5_Adipose_S7_L003_R1_001.fastq.gz C_5_Adipose_S7_L004_R1_001.fastq.gz	fastq fastq fastq fastq	2563785525.0	34183807.0	C 5 Adipose S7 L001 R1 001.fastq.gz	0:75	A:637947469;C:605870631;G:628121912;T:691743073;N:102440	75	637947469	605870631	628121912	691743073	102440	SRX21167052	SRS18428837	SRA1681062	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.96664	0.02865	0.834	0.27971	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-26	Adult	Adult	Adipose Tissue	Adipose Tissue
77258	77258	SRR25432806	SRX21167051	SRS18428836	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.	Adipose tissue Control diet Fish 3	C 4 Adipose	strain:AB\|age:Adult\|collection date:2022 11 18\|geo loc name:USA: Baltimore\|sex:female\|tissue:Adipose\|treatment:Control diet\|Replicate:Fish 3\|BioSampleModel:Model organism or animal	Adipose tissue Control diet Fish 3	C 4 Adipose	C 4 Adipose	Total RNA was extracted using Direct zol RNA Microprep Kits R2061 Zymo Research Irvine CA USA. Library was prepared using TruSeq Stranded mRNA Library Prep Kit Illumina San Diego USA	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	C_4_Adipose_S4_L004_R1_001.fastq.gz C_4_Adipose_S4_L003_R1_001.fastq.gz C_4_Adipose_S4_L002_R1_001.fastq.gz C_4_Adipose_S4_L001_R1_001.fastq.gz	fastq fastq fastq fastq	3511623000.0	46821640.0	C 4 Adipose S4 L001 R1 001.fastq.gz	0:75	A:856293655;C:770266027;G:990546207;T:894381906;N:135205	75	856293655	770266027	990546207	894381906	135205	SRX21167051	SRS18428836	SRA1681062	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.94775	0.0628	0.7667	0.53126	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-26	Adult	Adult	Adipose Tissue	Adipose Tissue
77259	77259	SRR25432807	SRX21167050	SRS18429003	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.	Adipose tissue Control diet Fish 2	C 3 Adipose	strain:AB\|age:Adult\|collection date:2022 11 18\|geo loc name:USA: Baltimore\|sex:female\|tissue:Adipose\|treatment:Control diet\|Replicate:Fish 2\|BioSampleModel:Model organism or animal	Adipose tissue Control diet Fish 2	C 3 Adipose	C 3 Adipose	Total RNA was extracted using Direct zol RNA Microprep Kits R2061 Zymo Research Irvine CA USA. Library was prepared using TruSeq Stranded mRNA Library Prep Kit Illumina San Diego USA	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	C_3_Adipose_S3_L001_R1_001.fastq.gz C_3_Adipose_S3_L002_R1_001.fastq.gz C_3_Adipose_S3_L003_R1_001.fastq.gz C_3_Adipose_S3_L004_R1_001.fastq.gz	fastq fastq fastq fastq	2209388625.0	29458515.0	C 3 Adipose S3 L001 R1 001.fastq.gz	0:75	A:547516154;C:527046595;G:550708343;T:584030443;N:87090	75	547516154	527046595	550708343	584030443	87090	SRX21167050	SRS18429003	SRA1681062	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.94878	0.05665	0.77384	0.53783	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-26	Adult	Adult	Adipose Tissue	Adipose Tissue
77260	77260	SRR25432808	SRX21167049	SRS18428835	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.	Adipose tissue Control diet Fish 1	C 1 Adipose	strain:AB\|age:Adult\|collection date:2022 11 18\|geo loc name:USA: Baltimore\|sex:female\|tissue:Adipose\|treatment:Control diet\|Replicate:Fish 1\|BioSampleModel:Model organism or animal	Adipose tissue Control diet Fish 1	C 1 Adipose	C 1 Adipose	Total RNA was extracted using Direct zol RNA Microprep Kits R2061 Zymo Research Irvine CA USA. Library was prepared using TruSeq Stranded mRNA Library Prep Kit Illumina San Diego USA	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	SRP451621	C_1_Adipose_S1_L001_R1_001.fastq.gz C_1_Adipose_S1_L002_R1_001.fastq.gz C_1_Adipose_S1_L003_R1_001.fastq.gz C_1_Adipose_S1_L004_R1_001.fastq.gz	fastq fastq fastq fastq	1866120150.0	24881602.0	C 1 Adipose S1 L001 R1 001.fastq.gz	0:75	A:472323893;C:446150218;G:455337258;T:492239412;N:69369	75	472323893	446150218	455337258	492239412	69369	SRX21167049	SRS18428835	SRA1681062	Carnegie Insitution for Science\|Embryology	Carnegie Insitution for Science	1	0.94807	0.02138	0.76788	0.49111	75	B	usable mapping rate	illumina	miseq	unknown	poly_a	trueseq	bulk	unknown	unknown	United States	2023-07-26	Adult	Adult	Adipose Tissue	Adipose Tissue

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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");;