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| Status |
Public on May 16, 2018 |
| Title |
Role of liquid sugar in regulating the hepatic transcriptome in a high fat Western diet model of NAFLD |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: The goals of this study are to use hepatic transcriptome profiling (RNA-seq) to examine the role of liquid sugar consumption in the progression of NAFLD.
Methods: Hepatic mRNA profiles of 12-week chow (n=4), high fat Western diet (n=5), and high fat Western diet + fructose/sucore in the drinking water (n=5) fed mice were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: We mapped about 100 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the livers of mice. RNA-seq data confirmed stable expression of X known liver specific genes. Approximately 10% of the transcripts showed differential expression between the XXX, with a fold change ≥1.5 and p value <0.05. Altered expression of XX genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several pathways that may contribute to NAFLD progression. RNA-seq data had a linear relationship with qRT–PCR: a goodness of fit (R2) of xxxx.
Conclusions:
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| Overall design |
Hepatic mRNA profiles of chow, HFWD, and HFWD+F/S fed mice were generated by deep sequencing.
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| Contributor(s) |
Greene MW |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Oct 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael W Greene |
| E-mail(s) |
mwgreene@auburn.edu
|
| Organization name |
Auburn University
|
| Department |
Nutrition
|
| Street address |
260 Lem Morrison Dr
|
| City |
Auburn |
| State/province |
AL |
| ZIP/Postal code |
36849 |
| Country |
USA |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (14)
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| Relations |
| BioProject |
PRJNA351264 |
| SRA |
SRP092258 |
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