Comment[GEAAccession]	E-GEAD-819
MAGE-TAB Version	1.1
Investigation Title	Hepatic gene expression in CDAHFD-induced non-alcoholic steatohepatitis model mouse
Experiment Description	A choline-deficient amino acid defined high-fat diet (CDAHFD)-induced NASH model is a well-established and reproducible experimental animal model. However, the cause of hepatic fibrogenesis on this model remains unclear. This study aimed to clarify the phenotypic changes and causality between metabolic changes with hepatic fibrogenesis in the CDAHFD-fed mice. To characterize the phenotypic changes in the CDAHFD-fed mouse liver, we conducted transcriptomic analyses (RNA-seq). C57BL/6J male mice were given a choline-deficient L-amino acid defined (0.1% methionine) 60% kcal high-fat diet (CDAHFD; A06071302, Research Diets) for 0, 1, 4, 8, and 12 weeks. The age- and sex-matched acclimatized mice fed a standard chow diet (CRF-1; Oriental Yeast, Japan) were assigned to the control group (0 weeks). Total RNA was extracted from frozen liver samples using the RNeasy Mini kit (Qiagen). After RNA quantification and quality control, libraries were constructed using the TruSeq Stranded mRNA LT Sample Prep kit (Illumina). The NovaSeq 6000 (Illumina) sequence paired-end read length was set to 2x100 bp; raw data were processed and checked using the Galaxy system. The filtered data were mapped onto the Gencode reference genome (GRCm38.p6) and annotated using Gencode (M24).
Experimental Design	disease state design
Experimental Factor Name	growth_condition
Experimental Factor Type	growth_condition
Person Last Name	Hosono
Person First Name	Takashi
Person Affiliation	Laboratory of Nutrition and Physiology, Nihon University
Person Roles	submitter
Public Release Date	2025-11-26
PubMed ID	41274506
Protocol Name	P-GEAD-3056	P-GEAD-3057	P-GEAD-3058	P-GEAD-3059	P-GEAD-3060	P-GEAD-3061
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol	treatment protocol
Protocol Description	The mice were euthanized by carbon dioxide inhalation, and tissues were collected and snap-frozen in liquid nitrogen.	Total RNA was extracted from frozen liver samples using the RNeasy Mini kit (Qiagen).	After RNA quantification and quality control, libraries were constructed using the TruSeq Stranded mRNA LT Sample Prep kit (Illumina).	The NovaSeq 6000 (Illumina) sequence paired-end read length was set to 2 x 100 bp.	Raw data were processed and checked using the Galaxy (ver. 20.01) system. FastQC ver. 0.72 was used for adapter trimming and quality filtering, fastp ver. 0.19.5 for alignment, and STAR ver. 2.7.1a for rRNA removal followed by application of bedtools (in the intersect mode) ver. 2.29.0 and featurecounts ver. 1.6.4 for quantification. The filtered data were mapped onto the Gencode reference genome (GRCm38.p6) and annotated using Gencode (M24).	Male 10-week-old C57BL/6J mice were given a choline-deficient L-amino acid defined (0.1% methionine) 60% kcal high-fat diet (CDAHFD; A06071302; Research Diets) for 0, 1, 4, 8, and 12 weeks. The age- and sex-matched acclimatized mice fed a standard chow diet (CRF-1; Oriental Yeast, Japan) were assigned to the control group (0 weeks).
SDRF File	E-GEAD-819.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB12803
Comment[Last Update Date]	2025-11-26