Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1002560 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25532317_1.fastq.gz | Fastqsanger.gz | |||
| SRR25532317_2.fastq.gz | Fastqsanger.gz | |||
| SRR25532318_1.fastq.gz | Fastqsanger.gz | |||
| SRR25532318_2.fastq.gz | Fastqsanger.gz | |||
| SRR25532319_1.fastq.gz | Fastqsanger.gz |
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Project description:During lactation, mammary epithelial secretory cells secrete huge amounts of milk from their apical side. The major milk proteins, the caseins, are secreted by exocytosis, while milk fat globules are released by budding, enwrapped by the plasma membrane. Due to the number and large size of milk fat globules, the membrane surface needed for their secretion might exceed that of the apical plasma membrane. In order to identify the cellular compartments that may provide membrane during the budding of milk fat globules, a large-scale proteomics analysis of both cytoplasmic lipid droplets and secreted milk fat globules membranes was performed in mouse cells. The differential analysis of the protein profiles of these two organelles strongly suggest that, in addition to the apical plasma membrane, at least the endoplasmic reticulum, the secretory vesicles containing caseins, and potentially the mitochondria contribute to the formation of the milk fat globule membrane. Moreover, the specific analysis of the membrane-associated as well as the raft-associated proteins reinforces this possibility and points to a role for lipid rafts in milk product secretion. The subcellular localization of several major proteins of the cytoplasmic lipid droplets or of the milk fat globule membrane was investigated by immunofluorescence in lactating mammary epithelial cells. Furthermore, the localization of GM1 ganglioside, a known marker of lipid rafts and of free cholesterol, showed a clear association with both cytoplasmic lipid droplets and secreted milk fat globules. Additionally, the presence of some SNARE proteins that may be involved in casein exocytosis and of two Rab GTPases on both cytoplasmic lipid droplets and milk fat globules was demonstrated by immunofluorescence. Altogether, our results provide evidence for a pivotal role of the endoplasmic reticulum as membrane contributor to milk fat globule budding, and suggest that some SNARE proteins may spatio-temporally coordinate the secretion of milk products.
2018-10-19 | PXD001024 | Pride
Project description:Long non-coding RNAs (lncRNAs) have been identified in various tissues and cell types from human, monkey, porcine and mouse. However, expression profile of lncRNAs across Guangxi native cattle and swamp buffalo muscle development has never been investigated. Here, we examine the expression of lncRNA in cattle and buffalo muscle at adult stage(12 months), exhibiting the first report of lncRNA in the Guangxi native cattle and swamp buffalo muscle development of a large animal. 16,236 lncRNA candidates were obtained from buffalo skeletal muscle samples, of which a number of lncRNAs were highly abundant, and 2,161 lncRNAs were differentially expressed between buffalo and cattle. Real-time quantitative PCR (qPCR) analysis confirmed the expression profile of these lncRNAs, including several highly abundant lncRNAs, and a subset of differently expressed lncRNAs according to the high-throughput RNA sequencing (RNA-seq) data. These results indicate that abundant lncRNA is differentially expressed in bovine muscle, indicating important and diverse functions in mammalian muscle development.
2019-12-20 | GSE123869 | GEO
Project description:The 4 day gene expression profile in the lactating mammary gland was demonstrated using the Human Ref-8 BeadChip array (Illumina, Inc). Of the 22,184 gene transcripts on the array, 14,070 genes were consistently expressed and represented the milk fat globule transcriptome. Milk protein genes were among the most highly expressed along with genes involved in the milk syntesis processes. Serial milk samples were collected every 3h for 4 days from 5 normal, lactating women. RNA was isolated from the milk fat globules and utilized for microarray analyses.
2011-06-30 | E-GEOD-15208 | biostudies-arrayexpress
Project description:Feed regimens have a pivotal role in modulating the transcriptional programs that, in turns, have an impact on many biological processes, including metabolism, health and development. Green feed diet in ruminant exerts a beneficial effect on rumen metabolism and enhances the content of health-promoting biomolecules in the milk. However, a comprehensive analysis focused to the identification of genes, and therefore, biological processes modulated by the green feed diet in buffalo rumen has never been reported so far. In this regard, to highlight the impact of the green feed diet on ruminal transcriptomic profiles, we performed RNA-sequencing in buffaloes fed a total mixed ratio (TMR) + the inclusion of 30% of ryegrass green feed (treated group) in comparison with buffaloes fed a dry TMR diet (control group).
2023-03-21 | GSE207815 | GEO
Project description:Pasteurized whole cow milk (Grade A) was purchased from the supermarket. Whole cow milk was centrifuged at 3 000 g at 4°C for 30 min and the fat layer was recovered. The recovered fat was washed with PBS for 20 min at 37°C, and the resuspened mixture was centrifuged again to obtain the milk fat. The wash procedure was repeated three times. Finally, milk fat was washed with MilliQ water to recover the fat globules. Milk fat globules were solubilized with a SDS solution (100 mM Tris-HCl, pH 7.4, 100 mM DTT and 4% SDS) and then incubated in 95°C water bath for 10 min. The mixtures were centrifuged at 14 000 g for 15 min, and the protein samples were collected. S-Trap, FASP, in-gel, and traditional Chl/MeOH, as well as modified chloroform/methanol (Chl/MeOH) or acetone precipitation followed by in-solution digestion without clean-up of tryptic peptides methods were applied to characterization cow MFGM proteome.
2018-10-19 | PXD009288 | Pride
Project description:The proteins of the milk fat globule membrane (MFGM) have a number of functions, such as the regulation of milk fat secretion and metabolism, the uptake and transportation of fatty acids in the intestine and potential protection from bacterial or viral infection. While the proteome of the MFGM in bovine milk has been extensively characterised, our knowledge of these proteins in buffalo milk is limited. In this study, a proteomic approach was used to characterise the proteome of the buffalo MFGM. Multiple extraction techniques were employed to increase the coverage of proteins identified, while label free relative quantitative liquid chromatography tandem mass spectrometry was used for comparison between the buffalo and bovine MFGM proteome. A total of 220 buffalo MFGM proteins and 234 bovine MFGM proteins were identified after being filtered from the initial dataset of 757 and 680 proteins respectively. Significantly greater amounts of xanthine oxidoreductase, platelet glycoprotein 4, heat shock cognate and calcineurin B homologous protein were identified per mass of buffalo MFGM protein extracted. The higher expression of xanthine oxidase in the MFGM of buffalo milk was confirmed by Western blot analysis and a heterogeneous distribution of this protein observed in situ on the surface of the MFGM. The high concentration of fat in buffalo milk, together with the differences in the MFGM proteome indicate differences in the nutritional profile, biological function, and potential ease of processing of buffalo and bovine milk products.
2017-05-19 | PXD005318 | Pride
Project description:We have utilized the RNA isolated from breast milk fat globule (MFG) from lactating women from 6h to 42 days following delivery using the HumanHT-12 v4 Expression BeadChip (Illumina, Inc) to determine the temporal coordination of changes in gene expression in milk substrate synthesis processes. Of the 47,323 gene transcripts on the array, 16,623 transcripts were expressed. Major milk protein genes were among the most highly expressed and induced along with those involved in the metabolic and biosynthetic processes of carbohydrate and lipid. Milk fat synthesis mirrors expression of genes involved in fat synthesis, lipolysis and transport. In the lactose synthesis pathway, expression of α-lactalbumin mRNA was high already in the early milk and did not change. Lactose synthesis paralleled the induction of gene expression of proteins involved in UDP-galactose synthesis and transport. Serial milk samples were collected 6h following delivery, q12 h for the first 4 days and then weekly for 6 wks from 7 healthy, lean, exclusively breastfeeding women [7 x 15 = 105 samples]. RNA was isolated from the milk fat globules and utilized for microarray analyses.
2012-09-04 | E-GEOD-36936 | biostudies-arrayexpress
Project description:Bovine mastitis, predominantly caused by pathogenic Staphylococcus aureus, is a major impediment to milk production. Although its prevalence varies from cows to buffaloes, it lacks relevant markers that mark the phases and progression of the disease. Thus, the focus of this study was to identify key proteins that mark the transition from subclinical to clinical states in a species specific manner. Whey proteins isolated from healthy and S. aureus infected milk from both Holstein Friesian cow and Murrah buffalo were characterized by label free quantification using mass spectrometry. Collectively, 662 proteins were identified with atleast two peptides, of which 51 and 80 proteins were found significant by ANOVA (p value < 0.05) with increasing or decreasing trends in the disease progression in HF and Mu, respectively. Linear change in expression of proteins like haptoglobin and fibronectin in HF and spermadhesin and osteopontin in Mu correlated with the stage of the disease and progression in a species specific manner. Similarly, high mobility group proteins, angiogenin, cofilin-1 that were previously reported in oxidative stress were overexpressed whilemembers of ubiquitin family which remove aggregated proteins were downregulated during the progression of infection. Subsequently, selected differentially expressed proteins (e.g. osteopontin, CAP-1 and fibrinogen α) were validated by Western blot analysis. Results of this study provide deeper insights on whey proteome dynamics and a signature pattern indicative of disease progression.
2022-02-15 | PXD012289 | Pride
Project description:Breastfeeding is vital for reducing morbidity and mortality, yet exclusive breastfeeding rates are low, with insufficient milk supply being a major weaning factor whose molecular causes remain largely unknown. In this study, we collected fresh milk samples from 30 lactating individuals, classified as low, normal, or high milk producers at multiple postpartum stages, and conducted extensive genomic and microbiome analysis. Using bulk RNA sequencing on human milk fat globules (MFG), milk cells, and breast tissue, we found that MFG-derived RNA closely resembles RNA from milk luminal cells. Furthermore, bulk and single-cell RNA-seq revealed changes in the transcriptome and cellular content linked to milk production. We identified specific genes and cell-type proportions differing in low and high milk production. Infant microbiome diversity was affected by feeding type, but not by maternal milk supply. This study provides a comprehensive human milk transcriptomic catalog, identifies genes associated with milk production, and highlights MFG as a useful biomarker for milk transcriptome analysis.
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