Macrococcoides caseolyticum JCSC5402
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ABSTRACT:
PROVIDER: PRJDA20209 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We carried out a cross species cattle-sheep array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the sheep genome analysing animals of Italian dairy breeds (Sarda, Bagnolese, Laticauda, Massese and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs) covering about 10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and median equal to 77.6 kb and 55.9 kb, respectively. A comparative analysis between the identified sheep CNVRs and those reported in the cattle and goat genomes indicated that overlaps between sheep and goat and sheep and cattle CNVRs are highly significant (P<0.0001) suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Many sheep CNVs affect genes with important biological functions. Further studies are needed to evaluate the functional relevance of these CNVs.
2010-11-16 | GSE25122 | GEO
Project description:We carried out a cross species cattle-sheep array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the sheep genome analysing animals of Italian dairy breeds (Sarda, Bagnolese, Laticauda, Massese and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs) covering about 10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and median equal to 77.6 kb and 55.9 kb, respectively. A comparative analysis between the identified sheep CNVRs and those reported in the cattle and goat genomes indicated that overlaps between sheep and goat and sheep and cattle CNVRs are highly significant (P<0.0001) suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Many sheep CNVs affect genes with important biological functions. Further studies are needed to evaluate the functional relevance of these CNVs. In this study we made use of the high conservation and homology between the cattle and sheep genomes determined by their phylogenetic closeness to identify CNVs in sheep applying the same approach we carried out to identify CNVs in the goat genome. We used a custom tiling array including ~385,000 oligonucleotide probes designed on the Btau_4.0 version of the Bos taurus genome assembly and analysed genomic DNA samples of 11 sheep belonging to 6 different Italian dairy sheep breeds (2 Sarda, 2 Bagnolese, 2 Comisana, 2 Massese, 2 Laticauda and 1 Valle del Belice) compared to the reference DNA of another Sarda sheep.
2010-11-16 | E-GEOD-25122 | biostudies-arrayexpress
Project description:We performed mRNA-seq on 27 samples from the three tissues (heart, liver and kidney) across three species (cattle, sheep, goat)
2017-09-06 | GSE77020 | GEO
Project description:Macrococcoides caseolyticum Genome sequencing and assembly
| PRJNA795004 | ENA
Project description:Milk and soy are reported to contain bioactive molecules with antibacterial and immunomodulatory actions, which may be beneficial to people with IBD. The aim of this study was to determine whether diets containing ruminant milk or soy solids reduce intestinal inflammation in Il10-/- mice. Male Il10-/- mice and C57BL/6J mice were fed diets containing 40% (w/w) sheep, goat, or cow whole milk powder, 40% (w/w) soy solids (NOW® Foods Soy Milk Powder, Instant), or one of two control diets (casein-free modified-AIN76A or standard AIN76A) from 4 to 11 weeks of age. Diets were based on AIN76A, which was included as an inter-experimental control for inflammation. For all diets except AIN76A, total protein, fat, carbohydrate and energy were kept as similar as possible. Weight and food intake were measured throughout the experiment (three times weekly), and intestinal tissue was taken for histopathology evaluation of inflammation and analysis of gene expression. Analysis of mouse weight and feed intake both showed a significant strain-diet interaction: Il10-/- mice fed the cow and goat milk diets ate less and gained less weight than all the other diet groups. This diet effect was not evident for the C57BL/6J mice. Il10-/- mice on the cow and goat milk diets had reduced colon histological injury scores relative to those on the other diets. Il10-/- mice on the cow and goat milk diets also had reduced expression of many immune/inflammatory-related genes and pathways.
2019-12-01 | GSE39830 | GEO
Project description:Body weight (BW) is a critical economic trait for meat production in sheep. The current study aimed to perform a genome-wide association study (GWAS) to detect significant single-nucleotide polymorphisms (SNPs) that are associated with BW in Hu sheep.
2020-06-18 | GSE152717 | GEO
Project description:Milk-derived extracellular vesicles (mEVs) have been proved to play a critical role in intercellular communication, mainly through the microRNAs (miRNAs) that they carry, to regulate biological functions of the target cells. Given miRNAs are evolutionarily conserved, EVs present in commercial milk may play a role in the physiology and health consumers. It is therefore essential to know the effects of technological treatments such as skimming and spray drying on the EV content of milk powders and on the cargo of bioactive molecules, in particular miRNAs, that they convey. Since goat’s milk or goat milk based formulas are considered as a healthy alternative for infants with cow’s milk sensitivities, including allergy, we undertook to analyze the EV content of skimmed and unskimmed goat's milk powders and to characterize their RNA content, in particular their miRNomes. mEVs were isolated using an optimized protocol based on Size Exclusion Chromatography (SEC) and compared regarding morphology, number and size by Transmission Electron Microscopy (TEM) and Nanoparticle Tracking Analysis (NTA). Their RNA and protein content were determined and their miRNomes established, using RNA sequencing. In this study we demonstrated that goat milk powders, skimmed or not upstream the spray drying treatment, contained many mEVs, ranging from 5.4 1011 to 2.5 1012 particles per mL of reconstituted milk, with an average size between 136.8 and 160.6 nm. We also demonstrated that mEVs carried significant amounts of RNA, including miRNAs. Using RT-qPCR, mRNAs encoding five of the major milk proteins were detected, suggesting that mEVs originated from mammary epithelial cells. We established the goat milk powder miRNome by identifying 351 miRNAs of which 233 are common to the 262 miRNAs previously profiled in raw goat milk. The 20 most abundant miRNAs (TOP 20) account for 80% of the total reads and the hierarchy of this TOP 20 miRNAs is somewhat overturned when comparing goat milk powder and raw goat milk. Surprisingly, whereas the comparison of raw from cow and goat milk confirmed the prevalence of miR-148a, miR-21-5p and miR-26a/miR-30a-5p, let-7a-5p and let-7f, which occupied ranks 1 and 2, respectively, in powders, were relegated to ranks 6 and 10 and 5 and 11 in raw goat and cow milk, respectively. Conversely to what was previously reported, we provide evidence that: i) EVs of typical morphology are present in goat milk powders; ii) mEVs survived the technological processes used to produce the powders; iii) their miRNA cargo is protected from degradation even though their miRNomes are not an exact mirror of miRNomes of EVs derived from fluid raw milk.
2025-01-01 | GSE254484 | GEO
Project description:Our analysis revealed the unique and common lncRNA-miRNA-mRNA networks of two kinds of adipocytes. Several lncRNAs that regulate goat meat quality were identified, such as XR_001918647.1, XR_001917728.1, XR_001297263.2 and LNC_004191. Our study utilized RNA-seq analysis to predict the functions of lncRNA on goat meat quality. Furthermore, our findings of lncRNA-miRNA-mRNA network, may contribute to a better understanding of the molecular mechanisms underlying in goat meat quality and provide a theoretical basis for further goat molecular breeding.
2021-12-25 | GSE186988 | GEO