Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Methionine restriction alleviate cognitive dysfunction in Alzheimer’s disease: the mediating roles of gut microbiota-brain axis

ABSTRACT: We reported that a 4-month methionine-restricted diet (MR) intervention reduced the cognitive impairment in Alzheimer’s disease. Here, we introduce the transcriptomics data of the mouse hippocampus to further study how MR regulates important biological processes and pathways. After mapping clean RNA-seq reads of all mice against the Mus musculus genome, we detected 56,412 genes (including 12,527 new predicted genes) with fragments per kilobase of transcripts per million mapped reads (FPKM) value. Gene set enrichment analysis (GSEA) was used for pathway or functional analysis of RNA-seq data.

ORGANISM(S): Mus musculus

PROVIDER: GSE164618 | GEO | 2021/12/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Methionine restriction alleviates age-associated cognitive decline via fibroblast growth factor 21

Project description:We reported a 3-month MR intervention alleviated age-related cognitive impairment. Here we present transcriptomics data of mice hippocampus to further investigate how MR regulates vital biological processes and pathways. After mapping clean RNA-seq reads of all mice against the Mus musculus genome, we detected 13,218 genes (including 3,187 new predicted genes with no annotation) with fragments per kilobase of transcripts per million mapped reads (FPKM) value. Gene set enrichment analysis (GSEA) was used for pathway or functional analysis of RNA-seq data.

2021-12-31 | GSE164097 | GEO

Effects of intermittent fasting on the cognitive impairment in Alzheimer's disease mice: the roles of the gut brain axis regulation mechanism

Project description:We reported a 16-week intermittent fasting intervention alleviated cognitive impairment in Alzheimer's disease. Here we present transcriptomics data of mice hippocampus to further investigate how intermittent fasting regulates vital biological processes and pathways. After mapping clean RNA-seq reads of all mice against the Mus musculus genome, we detected 56,412 genes (including 12,527 new predicted genes) with fragments per kilobase of transcripts per million mapped reads (FPKM) value. Gene set enrichment analysis (GSEA) was used for pathway or functional analysis of RNA-seq data.

2021-12-31 | GSE164461 | GEO

Pharmacologic IRE1/XBP1s Activation Promotes Systemic Adaptive Remodeling in Obesity

Project description:RNA was isolated from livers of DIO mice treated with IXA4 or vehicle (n=4 per condition) using the Zymo Research Quick-RNA Miniprep Kit according to the manufacturer’s instructions. RNA sequencing was performed by BGI Americas on the BGI proprietary platform (DNBseq), providing single-end 50 bp reads at 20 million reads per sample. Alignment of the sequencing data to the Mus musculus MGSCv37 NCBI build 37.2 was performed using DNAstar Lasergene SeqManPro. Assembled data were then imported into ArrayStar 12.2 with QSeq (DNAStar Inc) to quantify gene expression and normalized reads per kilobase million (RPKM). Differential expression analysis and statistical significance calculations between conditions were assessed using DESeq in R using a standard negative binomial fit for the aligned counts data and are described relative to the indicated control

2022-01-08 | GSE162567 | GEO

Spiny mice (Acomys cahirinus) activate unique transcriptional programs after severe kidney injuries and regenerate organ function without fibrosis

Project description:Purpose: The goal of this study was to characterize the kidney transcriptome of Mus musculus and Acomys cahirinus after unilateral ureteral obstruction (UUO) kidney injury. Methods: Kidney mRNA-seq profiles of 10 week old mouse and spiny mouse were generated at 2 day and 5 days after unilateral ureteral obstruction injury in triplicate, using Illumina NovaSeq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with Salmon, edgeR and a limma-voom pipeline in R. Results: For both Mus musculus and Acomys cahirinus kidneys, we mapped about 50 million sequence reads per sample to the mouse transcriptome and identified 20580 transcripts in kidneys of Mus musculus and 54075 transcripts in the kidneys of Acomys cahirinus. Using 1.5 fold change and FDR < 0.05, number of transcripts that are significantly different between Mus musculus samples: 3915 between normal and day 2 after UUO, 5365 between normal and day 5 after UUO. For Acomys cahirinus: 1765 between normal and day 2 after UUO, 2499 between normal and day 5 after UUO. Conclusions: Our study demonstrate there were many conserved responses to kidney injury between M. musculus and A. cahirinus despite the divergent outcomes for kidney fibrosis.

2021-09-13 | GSE168876 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Thymic Transcriptomes from Wild Type and Mir-146a Transgenic Mice

Project description:Purpose: To find out the global transcriptomic change induced by overexpression of miR-146a in thymus Methods:Thymic mRNA profile of two pools from age (five to six-week old)- and gender (one male and one female for each pool)- matched wild-type (WT) and miR-146a transgenic (Tg) mice were generated by deep sequencing using Illumina HiSeq 2500. The clean reads that passed quality filters were mapped against Mus musculus genome using HotHap2, and the only uniquely mapped reads were used to calculate reads per kilobase of exon per million fragment (RPKM) values for each sample. The transcript isoform with a fold-change over 2 and q<0.001 were considered differentially expressed. Conclusion: Our study identified 101 differently expressed transcripts in thymus from miR-146a Tg mice, including 56 down-regulated transcripts covering 49 genes which are the candidate targets of miR-146a

2018-02-14 | GSE99428 | GEO

Contrasting patterns of expression divergence in early and late stages of population divergence in mice

2006-12-13 | GSE2597 | GEO

Contrasting patterns of expression divergence in early and late stages of population divergence in mice

Project description:We compared gene expression differences in the polytypic species complex Mus musculus (Mus musculus musculus, Mus musculus domesticus, Mus musculus castaneus and Mus musculus ssp) with that of Mus spretus via oligonucleotide microarrays representing more than 20,000 genes. Analysis of the results by two way ANOVA statistics suggests that the most genes with significant differences in expression levels among the subspecies are found in liver and kidney and the least in testis. This picture is different when one compares with Mus spretus, where the largest number of differences is found in testis. The design we employed is a reference design. All tissues were hybridized against a pool of that same tissue from 9 C57BL6 mice. All mice were roughly 12 weeks of age. To control for biological variation, we have used several individual males from each sub-species. RNA was isolated from three different organs, namely brain, liver/kidney and testis.

2010-06-30 | E-GEOD-2597 | biostudies-arrayexpress

Variation in mouse chemical signals is genetically controlled and environmentally modulated

Project description:Urine proteomes of the house mouse (Mus musculus musculus, M. m. domesticus, M. m. castaneus).

2023-07-20 | PXD037086 | Pride

Hog1 controls global reallocation of RNA Pol II upon osmotic shock

Project description:When challenged with osmotic shock, S. cerevisiae induces hundreds of genes, despite a global reduction in transcriptional capacity. The mechanisms that regulate this rapid reallocation of transcriptional resources are not known. Here we show that redistribution of RNA Pol II upon stress requires the stress-responsive MAP kinase Hog1. We find that Hog1 and RNA Pol II co-localize to open reading frames that bypass global transcriptional repression, and that these targets are specified by two osmotic stress-responsive transcription factors. The combination of reduced global transcription with a gene-specific override mechanism allows cells to rapidly switch their transcriptional program in response to stress. ChIP-sequencing of S. cervisiae RNA Pol II, Hog1, Sko1 and Hot1 Processed data file descriptions: ORFcounts.txt: table of summed ChIP-seq reads that align to each ORF (normalized by reads per kilobase per million) promoter_counts.txt: table of summed ChIP-seq reads that align to each promoter (1kb upstream, normalized by reads per kilobase per million) downstream_counts.txt: table of summed ChIP-seq reads that align 3' regions (50-500 bp downstream, normalized by reads per kilobase per million) Sko1_peak_list.txt: table of peaks found by PeakSeq Hot1_peak_list.txt: table of peaks found by PeakSeq

2012-07-15 | E-GEOD-38208 | biostudies-arrayexpress

RNA sequencing of Mus musculus thymic lymphomas [ATM and RAG2]

Project description:RNA sequencing of Mus musculus thymic lymphomas

2020-12-30 | GSE121739 | GEO