run_metadata: 19475

This data as json

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19475	ERR14031292	ERX13434258	ERS22545282	ERP166767	PRJEB83101	Fish tales of fatty liver A transcriptomic approach to understanding NAFLD	inda-STUDY-IIITD-2024-11-18 13:55:50.21-189	Other	Background: Non alcoholic fatty liver disease is a significant global health concern affecting millions and characterized by its complexity as a multifaceted disease. Despite its prevalence the underlying molecular mechanisms remain poorly understood. Methods: Here we propose a novel diet induced zebrafish model to investigate NAFLD. We validate this model through a series of histological examinations and molecular assessments allowing us to explore the intricate pathways involved in the disease. We employ transcriptomic analysis to identify novel players associated with NAFLD progression. Results: Our findings demonstrate that zebrafish subjected to a high fat diet exhibit weight gain while Oil Red O staining confirms significant fat deposition in the liver. Quantitative PCR analysis reveals increased expression of lipogenic genes such as acc fasn hmgcs1 hmgcra alongside markers of endoplasmic reticulum stress such as atf6 xbp1 gadd45a ddit3 and mitochondrial unfolded protein response genes such as hspd1 hspa9 clpp lonp1 indicating mitochondrial dysfunction which includes increased expression of genes encoding oxphos complexes uqcrc2 cox4i1 atp5f1b. Transcriptomic profiling uncovers novel markers such as inha gck ces2a id3 and dysregulated pathways related to metabolism insulin signaling and cellular stress responses. Conclusions: This study successfully establishes a zebrafish model that replicates key features of NAFLD including histopathological changes and metabolic dysregulation. The validation of our model allows for a deeper exploration of the molecular landscape of NAFLD. By revealing novel biomarkers and pathways through transcriptomic analysis our research opens new avenues for understanding the pathogenesis of NAFLD and potential therapeutic targets.	ENA FIRST PUBLIC:2024 12 05\|ENA LAST UPDATE:2024 12 05		RNA Seq NAFLD Replicate 1	NAFLD Replicate 1	SAMEA117477678	Kusuma School of Biological Sciences (KSBS),IIT-Delhi;Department of Computational Biology,IIITD;IISER-Bhopal;Centre for Integrative Genomics,Genopode, University of Lausanne, Lausanne 1015, Switzerland	ENA first public:2024 12 05\|INSDC center name:Kusuma School of Biological Sciences KSBS IIT Delhi;Department of Computational Biology IIITD;IISER Bhopal;Centre for Integrative Genomics Genopode University of Lausanne Lausanne 1015 Switzerland\|INSDC status:public\|Submitter Id:SAMIN0009307 NAFLD Replicate 1\|broker name:IBDC\|collection date:2023 04 18\|common name:zebrafish\|geographic location country and/or sea:India\|sample name:SAMIN0009307 NAFLD Replicate 1\|scientific name:Danio rerio									Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD	Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9485	1	1	NaN		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP166767	Illumina HiSeq X paired end sequencing; Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD	ENA FIRST PUBLIC:2024 12 05\|ENA LAST UPDATE:2024 12 05	19073_NAFLD_11_R1.fastq.gz 19074_NAFLD_11_R2.fastq.gz	fastq fastq	11885531932.0	39356066.0	RUN Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9485	0:151 1:151	A:3208478929;C:2671086650;G:2843156238;T:3153091073;N:9719042	151	151			3208478929	2671086650	2843156238	3153091073	9719042	ERX13434258	ERS22545282	ERA31000101	Indian Biological Data Centre\|European Nucleotide Archive	Indian Biological Data Centre												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		India	2024-12-05	Undetermined	Undetermined	Liver	Liver and Biliary System