Project description:This study aimed to investigate transcriptional differences between liver tumours that were chemically-induced in five strains and species of mouse and rat. Male mice (Mus musculus domesticus C3H/HeOuJ and C57BL/6J, Mus musculus castaneus CAST/EiJ, and Mus Caroli CAROLI/EiJ) and rats (Fischer F344) were treated with diethylnitrosamine (DEN) to induce liver tumours. After tumour dissection, genomic DNA and RNA were simultaneously isolated and purified for library preparation and sequencing. Additional liver tissue samples were collected and processed in parallel: untreated liver from infant mice (15-day old, P15) and juvenile rats (56-day old, P56); untreated adult liver tissue; DEN-exposed adult liver tissue; spontaneous liver tumours.
Project description:Liver samples were isolated from postnatal day 15 (P15) untreated mice and then flash frozen: Mus musculus musculus (C57BL/6J), Mus musculus castaneus (CAST), and Mus caroli (CAROLI). DEN-induced liver tumours and background liver tissue were collected from 37-week old C57BL/6J mice. ATAC-seq was performed to identify the open regions of the genome.
Project description:We explored the microevolutionary trends of CTCF binding evolution by preforming ChIP-seq experiments in five closely related Mus strains, subspecies and species: Mus musculus domesticus, Mus musculus castaneus, Mus spretus, Mus caroli and Mus pahari. All experiments were performed in adult male liver samples in 3 biological replicates and with an input control set. Complementary RNA-seq data from this same study have been deposited in ArrayExpress under accession numebr E-MTAB-5768 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5768 ).
Project description:This study aims to investigate the interactions of mutagenic lesions from diethylnitrosamine (DEN) treatment of mouse and rat livers with cellular processes such as replication, transcription, and the interactions of DNA with proteins. Data are available for the following laboratory strains of mouse and rat: Mus musculus (C57BL/6J and C3H), Mus musculus castaneous (CAST), Mus caroli (CAROLI), and Rattus norvegicus (F344). Liver samples from untreated mice (postnatal day 15, P15) and rats (postnatal day 56, P56) were isolated and flash-frozen. ChIP-seq was performed to identify histone modification (H3K4me3 and H3K27ac) and CTCF binding sites in livers of ten pooled individuals (mice) or one individual (rat). The experiment was done with at least three biological replicates, plus matched input libraries. Data for CTCF binding in C3H mice is available at ArrayExpress (E-MTAB-11959).
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. Keywords: multi-species comparison
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.
