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| Status |
Public on Mar 10, 2017 |
| Title |
Next generation sequencing of RNA expression on total splenic B cells from NOD mice fed variable diets |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: The goals of this study is to examine if feeding NOD mice with diets supplemented with SCFAs causes altered gene expression in Splenic B cells
Methods: B cell RNA profiles from NOD.LT mice fed fed different diets, a non-purified diet (n=4), a high amylose diet (n=4), a high amylose diet supplemented with acetate (n=4) or a high amylose diet supplemented with butyrate (n=4) were generated by deep sequencing, in triplicate, by Illumina 100 - base HT mode the sequence reads that passed quality filters were summarized into gene models using featureCounts from the Rsubread package, and differential gene expression for the various contrasts between dietary treatments was identified using the EdgeR analysis in R
Results: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the mouse genome (build GRCm38) and identified 16,257 transcripts present in B cells from NOD.LT mice fed different diet.
Conclusions: Our study investigates how differing diets alter the expression of important genes in B cells, allowing us to further understand the role diets can play in modulating T1D development.
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| Overall design |
B cell mRNA profiles of 15 week NOD.LT mice fed either NP (N=4), HAMS (N=4), HAMSA (N=4) or HAMSB (N=4) were generated by deep sequencing, in triplicate, using ?.
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| Contributor(s) |
Marino E, McLeod KH, Wilson T, Archer S, Powell D |
| Citation(s) |
28346408 |
| |
| Submission date |
Feb 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kirill Tsyganov |
| E-mail(s) |
kirill.tsyganov@monash.edu
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| Phone |
+61399020256
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| Organization name |
Monash University
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| Department |
Monash Bioinformatics Platform
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| Street address |
Wellington Road
|
| City |
Clayton |
| State/province |
Victoria |
| ZIP/Postal code |
3800 |
| Country |
Australia |
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| Platforms (1) |
| GPL21493 |
Illumina HiSeq 3000 (Mus musculus) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA374020 |
| SRA |
SRP099204 |
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