Transcription profiling of Hfe-deficient liver and duodenum in mouse strains with differing susceptibilities to iron loading
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Marie-Paule Roth
PROVIDER: E-GEOD-7357 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Hfe disruption in the mouse leads to experimental hemochromatosis by a mechanism which remains elusive. Evidence for at least five modifier genes has been obtained. These account for the higher iron load of Hfe-deficient D2 mice compared to B6 mice. Gene expression profling was used to clarify the mechanism of Hfe action and to identify potential modifier genes. Keywords: response to genetic modification
2008-03-22 | GSE7357 | GEO
Project description:This dataset consists of whole brain samples from 10 B6 and 12 D2 mice, in order to assess the amount of strain-specific alternative splicing. This design consists of whole brain total RNA samples from 10 B6 and 12 D2 mice
2011-05-10 | E-GEOD-27282 | biostudies-arrayexpress
Project description:DBA/2J (D2) and C57BL/6J mice (B6) were infected intra-nasally with 2x10^3 FFU of influenza A H1N1 (PR8) virus. Lungs were collected from mock-infected controls or at day 1,2,3,4 post infection. Expression data were obtained from three independent experiments. We infected a highly susceptible mouse strain (D2) and a resistant strain (B6) with PR8 and performed a genome-wide expression analysis. We found genes expressed in lung epithelium that were specifically down-regulated in D2 mice, whereas a cluster of genes on chromosome 3 was only down-regulated in B6. In both mouse strains, chemokines, cytokines and interferon-response genes were up-regulated, indicating that the main innate immune defense pathways were activated. However, many immune response genes were up-regulated in D2 much stronger than in B6, and several immune response genes were exclusively regulated in D2. Thus, susceptible D2 mice showed a hyper-inflammatory response. This response is similar to infections with highly pathogenic influenza virus and may serve as a paradigm for a hyper-inflammatory host response to influenza A virus.
2011-12-01 | E-MTAB-835 | biostudies-arrayexpress
Project description:Purpose: The goal of the present study is to provide an independent assessment of the retinal transcriptome signatures of the C57BL/6J (B6) and DBA/2J (D2) mice and to enhance existing microarray datasets for accurately defining the allelic differences in the BXD recombinant inbred strains. Methods: Retinas from both B6 and D2 mice (3 of each) were used for the RNA-seq analysis. Transcriptome features were examined for both strains. Differentially expressed genes between the 2 strains were identified and bioinformatic analysis was performed to analyze the transcriptome differences between B6 and D2 strains, including Gene ontology (GO) analysis, Phenotype and Reactome enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The RNA-seq data were then directly compared with one of the microarray datasets (DoD Retina Normal Affy MoGene 2.0 ST RMA Gene Level Microarray Database) hosted on GeneNetwork (www.genenetwork.org). Results: RNA-seq provided an in-depth analysis of the transcriptome of the B6 and D2 retina with a total of more than 30,000,000 reads per sample. Over 70% of the reads were uniquely mapped, resulting in a total of 18,100 gene counts for all 6 samples. 1,665 genes were differentially expressed, with 858 of these more highly expressed in B6 and 807 more highly expressed in D2. Several molecular pathways were differentially active between the two strains, including the retinoic acid metabolic process, endoplasmic reticulum lumen, extracellular matrix organization, and PI3K-Akt signaling pathway. The most enriched KEGG pathways were the pentose and glucuronate interconversions pathway, the cytochrome P450 pathway, protein digestion and absorption pathway and the ECM-receptor interaction pathway. Each of these pathways had a more than 4-fold enrichment. The DoD normal retina microarray database provided expression profiling for 26,191 annotated transcripts for B6 mouse, D2 mouse and 53 BXD strains. A total of 13,793 genes in this microarray dataset were comparable to the RNA-seq dataset. For both B6 and D2, the RNA-seq data and microarray data were highly correlated with each other (Pearson's r = 0.780 for B6 and 0.784 for D2). Our results suggest that the microarray dataset can reliably detect differentially expressed genes between the B6 and D2 retinas, with a positive predictive value of 45.6%, and a negative predictive value of 93.6%. Examples of true positive and false positive genes are provided. Conclusions: Retinal transcriptome features of B6 and D2 mouse strains provide a useful reference for a better understanding of the mouse retina. Generally, the microarray database presented on GeneNetwork shows good agreement with the RNA-seq data, while we note that any allelic difference between B6 and D2 should be verified with the latter.
2019-05-31 | GSE127942 | GEO
Project description:To gain insight into the host cell types, cellular and molecular pathways possibly involved in the differential permissiveness to pulmonary replication of M. tuberculosis, we carried out transcript profiling studies on M. tuberculosis-infected lungs from congenic and parental strains. We were particularly interested in two groups of transcripts. The first group consists of transcripts which expression in the lung is regulated in response to M. tuberculosis infection (global response to infection), and that is obtained by comparing transcripts profiles of infected vs. uninfected lungs. The second group of transcripts is associated with increased resistance to M. tuberculosis infection of B6 and D2.B6-Chr7 mice. That list consists in the overlap between the lists commonly expressed in response to infection between resistant B6 and D2.B6-Chr7 but that show a significant difference in modulation when compared to infected susceptible D2.<br><br> In these experiments, B6, D2 as well as the D2.B6-Chr19, and D2.B6-Chr7 congenic lines were infected with M. tuberculosis and lungs were harvested at day 30 and day 70, and RNA was prepared. Three independent RNA samples from each group were converted to labeled cDNAs and hybridized to Affymetrix oligonucleotides arrays (Mouse Genome 430 2.0 array). Hybridization results were analyzed with the Genesifter analysis program to characterize changes in gene expression.
2009-02-20 | E-MEXP-1942 | biostudies-arrayexpress
Project description:This dataset consists of whole brain samples from 10 B6 and 12 D2 mice, in order to assess the amount of strain-specific alternative splicing.
2011-05-10 | GSE27282 | GEO
Project description:C57BL/6J (B6) and DBA/2J (D2) mice were fed a high-fat/high-cholesterol diet in order to investigate the responses to that diet over time and their underlying genetic factors. We observed distinctly diverse responses between B6 and D2 mice, including dynamic distribution of cholesterol in serum and bile, hepatic apoptosis and dynamic formation of gallstones and atherosclerosis. Hepatic microarray analysis revealed distinctly different gene expression patterns in functional pathway groups including lipid metabolism, oxidative stress, immune/inflammation response and apoptosis, which might account for the different responses.This might provide us not only new insights into gallstones formation and atherosclerosis, but also opportunities to identify candidate genes for high-fat/high-cholesterol related diseases. C57BL/6J (B6) and DBA/2J (D2) mice were fed a high-fat/high-cholesterol diet in 0,1,4 12,21 weeks,respectively. Liver tissues of mice from each time-point were removed for RNA extraction. Equal amounts of RNA samples from five mice of each strain at each time-point were pooled and then used to generate biotinylated cRNA targets for Affymetrix GeneChip Mouse Genome 430 2.0 Array.
2014-12-14 | E-GEOD-17810 | biostudies-arrayexpress
Project description:C57BL/6J (B6) and DBA/2J (D2) mice were fed a high-fat/high-cholesterol diet in order to investigate the responses to that diet over time and their underlying genetic factors. We observed distinctly diverse responses between B6 and D2 mice, including dynamic distribution of cholesterol in serum and bile, hepatic apoptosis and dynamic formation of gallstones and atherosclerosis. Hepatic microarray analysis revealed distinctly different gene expression patterns in functional pathway groups including lipid metabolism, oxidative stress, immune/inflammation response and apoptosis, which might account for the different responses.This might provide us not only new insights into gallstones formation and atherosclerosis, but also opportunities to identify candidate genes for high-fat/high-cholesterol related diseases.
2014-12-14 | GSE17810 | GEO
Project description:We previously utilized interval-specific congenic lines derived from C57BL/6J (B6) and DBA/2J (D2) alleles to fine map a quantitative trait locus (QTL) influencing methamphetamine (MA)- induced locomotor activity. We identified a 0.23 MB critical interval on chromosome 11 containing only two protein coding genes, Rufy1 and Hnrnph1. Notably, Rufy1 contains three missense SNPs and Hnrnph1 contains 1 SNP near the 5â UTR. In an effort to identify the molecular mechanisms that bridge genetic variation with behavior, we conducted transcriptome analysis via mRNA sequencing (RNA-seq) in a B6.D2 congenic line (chr.11: 50-60 Mb) that captures the QTL. There was an overrepresentation of cis-regulated, differentially expressed genes within the congenic interval (4 out of 92 differentially expressed genes; FDR < 0.05) and widespread genomic regulation on all autosomes. For this study, 3mm punches from both striatal hemispheres were collected and pooled from 16 mice (8 controls and 8 B6.D2 congenics), and RNA was extracted and prepared for cDNA library preparation using the Illumina TruSeq (oligo-dT; 50bp single-end reads). Samples 1-16, consisting of alternating B6 and B6.D2 congenics were run in four lanes total, with samples 1-8 run in duplicate across lanes 5 and 6 and samples 9-16 acorss lanes 7 and 8, respectively. Raw samples provided are labeled with the "CB-" prefix, followed by the sample number and the lane that it was run in is described at the tail end as "_L00#" with # being either lane 5, 6, 7 or 8. In this study, all odd samples (e.g. CB-1,3,5 etc.) are C57BL/6J littermate controls, while all even samples are B6.D2 congenics. Note that the lane 7 replicate for Sample CB-13 (CB-13_L007.fastq.gz) was not processed due to technical difficulties with the file.
2015-12-11 | E-GEOD-66366 | biostudies-arrayexpress