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Series GSE94774 Query DataSets for GSE94774
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
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.
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 ?.
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
Phone +61399020256
Organization name Monash University
Department Monash Bioinformatics Platform
Street address Wellington Road
City Clayton
State/province Victoria
ZIP/Postal code 3800
Country Australia
Platforms (1)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (16)
GSM2482748 GD1
GSM2482749 GD3
GSM2482750 GD4
BioProject PRJNA374020
SRA SRP099204

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Supplementary file Size Download File type/resource
GSE94774_ReverseStrandedCounts-withNames.txt.gz 834.0 Kb (ftp)(http) TXT
GSE94774_ReverseStrandedCounts.txt.summary.txt.gz 676 b (ftp)(http) TXT
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