Whole genome sequence of a C57BL/6J mouse
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR929742_1.fastq.gz | Fastqsanger.gz | |||
| ERR929742_2.fastq.gz | Fastqsanger.gz | |||
| ERR929743_1.fastq.gz | Fastqsanger.gz | |||
| ERR929743_2.fastq.gz | Fastqsanger.gz | |||
| ERR929744_1.fastq.gz | Fastqsanger.gz |
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Project description:The neuropeptide arginine vasopressin (AVP) plays significant roles in maintaining homeostasis and regulating social behavior. In vaginally delivered neonates, a surge of AVP is released into the bloodstream at levels exceeding release during life-threatening conditions such as hemorrhagic shock. It is currently unknown where the potential sites of action are in the neonate for these robust levels of circulating AVP at birth. The purpose of this study is to identify the location of AVP receptor 1a (AVPR1A) sites as potential peripheral targets of AVP in the neonatal mouse. RT-qPCR analysis of a sampling of tissues from the head demonstrated the presence of Avpr1a mRNA, suggesting local peripheral translation. Using competitive autoradiography in wildtype (WT) and AVPR1A knockout (KO) postnatal day 0 (P0) male and female mice on a C57BL/6J background, specific AVPR1A ligand binding was observed in the neonatal mouse periphery in sensory tissues of the head (eyes, ears, various oronasal regions), bone, spinal cord, adrenal cortex, and the uro-anogenital region in the neonatal AVPR1A WT mouse, as it was significantly reduced or absent in the control samples (AVPR1A KO and competition). AVPR1A throughout the neonatal periphery suggest roles for AVP in modulating peripheral physiology and development of the neonate.
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Project description:BackgroundIntestinal microorganisms affect host physiology, including ageing. Given the difficulty in controlling for human studies of the gut microbiome, mouse models provide an alternative avenue to study such relationships. In this study, we report on the complete genome of "Faecalibaculum rodentium" ALO17, a bacterium that was isolated from the faeces of a 9-month-old female C57BL/6J mouse. This strain will be utilized in future in vivo studies detailing the relationships between the gut microbiome and ageing.ResultsThe whole genome sequence of "F. rodentium" ALO17 was obtained using single-molecule, real-time (SMRT) technique on a PacBio instrument. The assembled genome consisted of 2,542,486 base pairs of double-stranded DNA with a GC content of 54.0 % and no plasmids. The genome was predicted to contain 2794 open reading frames, 55 tRNA genes, and 38 rRNA genes. The 16S rRNA gene of ALO17 was 86.9 % similar to that of Allobaculum stercoricanis DSM 13633(T), and the average overall nucleotide identity between strains ALO17 and DSM 13633(T) was 66.8 %. After confirming the phylogenetic relationship between "F. rodentium" ALO17 and A. stercoricanis DSM 13633(T), their whole genome sequences were compared, revealing that "F. rodentium" ALO17 contains more fermentation-related genes than A. stercoricanis DSM 13633(T). Furthermore, "F. rodentium" ALO17 produces higher levels of lactic acid than A. stercoricanis DSM 13633(T) as determined by high-performance liquid chromatography.ConclusionThe availability of the "F. rodentium" ALO17 whole genome sequence will enhance studies concerning the gut microbiota and host physiology, especially when investigating the molecular relationships between gut microbiota and ageing.
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Project description:SINGLE PICOEUKARYOTES WHOLE GENOME SEQUENCE
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Project description:The Chinese Kunming (KM) mouse is a widely used outbred mouse stock in China. However, its genetic structure remains unclear. In this study, we sequenced the genome of the C57BL/6J-Chr1KM (B6-Chr1KM) strain, the chromosome 1 (Chr 1) of which was derived from one KM mouse. With 36.6× average coverage of the entire genome, 0.48 million single nucleotide polymorphisms (SNPs) and 96,679 indels were detected on Chr 1 through comparison with reference strain C57BL/6J. Moreover, 46,590 of them were classified as novel mutations. Further functional annotation identified 155 genes harboring potentially functional variants, among which 27 genes have been associated with human diseases. We then performed sequence similarity and Bayesian concordance analysis using the SNPs identified on Chr 1 and their counterparts in three subspecies, Mus musculus domesticus, M. m. musculus, and M. m. castaneus. Both analyses suggested that the Chr 1 sequence of B6-Chr1KM was predominantly derived from M. m. domesticus while 9.7% of the sequence was found to be from M. m. musculus. In conclusion, our analysis provided a detailed description of the genetic variations on Chr 1 of B6-Chr1KM and a new perspective on the subspecies origin of KM mouse which can be used to guide further genetic studies with this mouse strain.
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Project description:Isogenic laboratory mouse strains enhance reproducibility because individual animals are genetically identical. For the most widely used isogenic strain, C57BL/6, there exists a wealth of genetic, phenotypic, and genomic data, including a high-quality reference genome (GRCm38.p6). Now 20 years after the first release of the mouse reference genome, C57BL/6J mice are at least 26 inbreeding generations removed from GRCm38 and the strain is now maintained with periodic reintroduction of cryorecovered mice derived from a single breeder pair, aptly named Adam and Eve. To provide an update to the mouse reference genome that more accurately represents the genome of today's C57BL/6J mice, we took advantage of long read, short read, and optical mapping technologies to generate a de novo assembly of the C57BL/6J Eve genome (B6Eve). Using these data, we have addressed recurring variants observed in previous mouse genomic studies. We have also identified structural variations, closed gaps in the mouse reference assembly, and revealed previously unannotated coding sequences. This B6Eve assembly explains discrepant observations that have been associated with GRCm38-based analyses, and will inform a reference genome that is more representative of the C57BL/6J mice that are in use today.
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Project description:Repetitive elements (REs) make up the vast majority of the mammalian genomes. We identified species-specific genomic libraries of RE arrays. The non-random configurations of RE arrays suggest their functions. We tested whether RE arrays undergo age- and tissue/cell-specific rearrangements. An RE array of C57BL/6J mice, containing tandem repeats of a mosaic of transposable REs, was selected to examine rearrangements in different ages and tissues. There were marked changes in the array configuration in the genomes of the skin and brain in all mice of six weeks and older, whereas the heart and liver had alterations at 29weeks. The temporal variations were confirmed by identifying putative rearrangement junctions. Temporal and spatial rearrangements of certain RE arrays may contribute to the acquired characteristics of the genome information system.
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Project description:Hematopoietic stem cells (HSC) are heterogeneous in their ability to durably reconstitute the blood system. Epigenome surveys along the hematopoietic hierarchy and within the HSC compartment have revealed distinct epigenomic states associated with functionally defined hematopoietic cell types. However, the degree to which epigenomic states vary within functionally defined hematopoietic populations is still largely unknown. To address this question we performed single-cell genome-wide DNA methylation profiling of linage negative Sca+cKit+ (LSK) and EPCR+CD45+CD48-CD150+ (ESLAM) hematopoietic stem cell populations purified from adult mouse bone marrow. For this we developed a bisulfite based whole genome protocol suitable for use on single index sorted mammalian cells. Analysis of the resulting data from 148 single cells revealed that the methylomes of single HSCs show characteristics consistent with those defined from bulk populations. Comparing methylation states across single HSCs revealed a significant reduction in CpG state adjacency compared to bulk estimates and that on average 13% of CpGs exist in the opposite methylation state between any two cells within both surface marker defined HSC containing populations. Utilizing a novel analytical approach designed to address missing data inherent in single cell assays we identified an epigenetically distinct subpopulation of cells present in both the LSK and ESLAM populations. Enrichment analysis of genes associated with this distinct epigenetic state revealed pathways consistent with hematopoietic stem cell function, and integration with single-cell RNA-seq data defined putative surface proteins that mark this population, including the previously identified hematopoietic marker, NRXN1.
2017-12-31 | GSE95697 | GEO
Project description:Whole genome sequence Genome sequencing and assembly
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Project description:Whole genome sequence Genome sequencing and assembly
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Project description:Regulation of body weight is an important strategy for small prey animals to avoid capture. Field and laboratory studies have shown that prey animals reduce body size when subjected to long-term predator stimuli. However, the causes of predator-induced weight regulation are highly variable and the underlying mechanisms remain unclear. Understanding this phenomenon is important for gaining a better understanding of how animals regulate body weight under ethologically relevant conditions and has implications for obesity. Here we expose inbred C57BL/6J mice to a fear-inducing odorant (2,4,5-trimethylthiazole; mT) to model predation-induced weight regulation. Eight week-old mice were put on a 45% high fat diet (HFD) or chow diet (5% fat) and exposed daily to mT, an equally aversive dose of butyric acid (BA), or a neutral control scent (almond). mT-exposed mice in both diet groups gained significantly less weight over a 6-week period than BA-exposed mice. This differential weight gain appears unlikely to be due to differences in food intake and activity level, or brown adipose thermogenesis between the mT and BA groups. However, following chronic mT exposure we find increases in ΔFosB protein, a marker for long-term neural plasticity, in the dorsomedial hypothalamus (DMH)-an area previously implicated in chronic stress and defensive responses, as well as weight regulation. This study establishes a simplified and robust laboratory model of predation-mediated weight regulation with inbred lab mice and fear-inducing odor, and suggests a likely, yet undetermined, metabolic adaptation as contributing to this response.
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