Transcriptome analysis of fat globules in milk of cows with differential genotype for β-casein
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1140630 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30008242_1.fastq.gz | Fastqsanger.gz | |||
| SRR30008242_2.fastq.gz | Fastqsanger.gz | |||
| SRR30008243_1.fastq.gz | Fastqsanger.gz | |||
| SRR30008243_2.fastq.gz | Fastqsanger.gz | |||
| SRR30008244_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 28 |
Similar Datasets
Project description:In the framework of A2 milk production, a better understanding of the molecular mechanisms of the milk synthesis is needed. The transcriptome profiling of mamamry gland of Holstein cows with A1A1 genotype (n = 7) and A2A2 genotype (n = 7) for β-casein was analysed by RNA-seq technology. Total RNA was isolated from milk fat globules (non-invasive source of mammary RNA). Out of the 11,180 and 11,257 genes expressed in milk fat globules (identified with DESeq2 and EdgeR packages, respectively), only two genes were detected as differentially expressed between A1A1 and A2A2 genotype cows, indicating that both groups had very similar mammary gland transcriptome profiles. The majority of the highly expressed genes in milk fat globulesduring lactation (FPKM ≥500) were involved in biological process and molecular functions related to protein synthesis and energy production, as lactation is one of the most energetically demanding process for female mammals.
2025-05-12 | GSE273229 | GEO
Project description:In dairy cows, milk production and composition are affected by numerous factors, including diet. Milk is the body fluid with the highest RNA concentration, including numerous microRNA. These microRNA presence in the different milk compartments is still poorly documented and the effect of feed restriction on milk miRNome has not been described yet. The aim of this study was to describe the effects of feed restrictions of different intensitizes on milk compartment miRNome composition. Two feed restriction trials were performed on lactating dairy cows, one of high intensity and one of moderate intensity. 2 896 mature microRNA were identified in milk, including 1 493 that were already known in bovine specie. Among the 1 095 miRNA that were abundant enough to be informative, 10% were exclusive to one milk compartment and the abundance of 155 varied between compartments, revealing a specific miRNome for each milk fraction. Feed restriction affected differently these miRNome, with microRNA in whole milk and milk extracellular vesicles being the most affected and microRNA in fat globules and exfoliated mammary epithelial cells being relatively or completely unaffected. Target prediction of known microRNA that varied under feed restriction reflected modification of some key pathways for lactation related to milk fat and protein metabolisms, cell cycle and stress responses. These findings open up opportunities for future research on the use of milk miRNA as biomarkers of energy status in dairy cows.
2023-05-31 | GSE207759 | GEO
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:Cows were fed a lactation diet at ad libitum intake (n = 6). At 27±3 days in milk, cows were injected with 50 µg of LPS E. coli in one healthy rear mammary quarter. Milk samples were collected just before LPS challenge (LPS-) and 6.5 h after LPS challenge (LPS+) from the same cows. Microarray analysis was performed using customized 8x60K ruminant miRNA microarrays to compare LPS- to LPS+ miRNome. MiRNome comparison between LPS- and LPS+ identified 37 differentially abundant miRNAs (q-value ≤ 0.05)
2023-10-23 | GSE229476 | GEO
Project description:Analysis of key genes and gene networks determining milk productivity of the dairy HF cows Transcriptomes were compared of in the mammary glands of the healthy lactating Holstein Friesian cows of the high- (average 11097 kg milk/lactation) and low- (average 6956 kg milk/lactation) milk yield.
2011-11-16 | E-GEOD-33680 | biostudies-arrayexpress
Project description:Human milk fat globules, by enveloping cell contents during their secretion into milk, are a rich source of mammary cell RNA. Here, we pair this non-invasive mRNA source with RNA sequencing technology to probe the milk fat layer transcriptome during three stages of lactation: colostral, transitional, and mature milk production. We find that transcriptional profiles cluster not by postpartum day, but by milk Na:K ratio, indicating that women sampled during the same postpartum time frame could be at markedly different stages of gene expression. Each stage of lactation is characterized by a dynamic range (105-fold) in transcript abundances not previously observed with microarray technology. We discovered that transcripts for isoferritins and cathepsins are strikingly abundant during colostrum production, highlighting the potential importance of these proteins for neonatal health. Two transcripts, encoding M-NM-2-casein (CSN2) and a-lactalbumin (LALBA), make up 45% of the total pool of mRNA in mature lactation. Genes significantly expressed across all stages of lactation are associated with making, modifying, transporting, and packaging milk proteins. Stage-specific transcripts are associated with immune defense during the colostral stage, up-regulation of the machinery needed for milk protein synthesis during the transitional stage, and the production of lipids during mature lactation. We observed strong modulation of key genes involved in lactose synthesis and insulin signaling. In particular, PTPRF may serve as a biomarker linking insulin resistance with insufficient milk supply. This study provides the methodology and reference data set to enable future targeted research on the physiological contributors to sub-optimal lactation in humans. Milk fat mRNA profiles were generated from Day 2 and mature milk samples obtained from lactating mothers
2013-07-22 | E-GEOD-45669 | biostudies-arrayexpress
Project description:The aim of the present study was to correlate lipid metabolism genes in the mammary gland tissue affected by stage of lactation and nutrition to the resulting milk fatty acids composition in grazing dairy cows, and to classify milk fatty acid (FA) groups based on variations in lipid metabolism gene expression patterns. Identifying the relationship between lipid metabolism genes in the mammary gland tissue and the resulting milk fatty acid composition is expected to greatly contribute to our understanding of milk fatty acid metabolism and to enhance opportunities to improve milk fat composition through nutrition. In fact, SNCA, SCD5, and PNPLA2 lipid metabolism-related genes affected by unsaturated fatty acids supplementation, were found to strongly correlated to different milk FA groups, but also contributed most to the classification of these FA groups, suggesting a significant role in mediating the lipid metabolism in the mammary gland tissue and determining the milk fatty acids composition. A total of 28 Holstein-Friesian dairy cows in mid-lactation were blocked according to parity (2.4 ± 0.63 years), days in milk (DIM; 153 ± 32.8 days), milk yield (25.7 ± 3.08 kg/d) and fat content (4.3 ± 0.12%). Cows were then randomly assigned to four UFA-sources based on rapeseed, soybean, linseed or a mixture of the three oils for 23 days (Period I) after which, all 28 cows were switched to a control diet for an additional 28 days (Period II). On the last day of both periods, mammary gland biopsies were taken to study genome-wide differences in lipid metabolism gene expression.
2011-01-01 | E-GEOD-20908 | biostudies-arrayexpress
Project description:Human milk fat globules, by enveloping cell contents during their secretion into milk, are a rich source of mammary cell RNA. Here, we pair this non-invasive mRNA source with RNA sequencing technology to probe the milk fat layer transcriptome during three stages of lactation: colostral, transitional, and mature milk production. We find that transcriptional profiles cluster not by postpartum day, but by milk Na:K ratio, indicating that women sampled during the same postpartum time frame could be at markedly different stages of gene expression. Each stage of lactation is characterized by a dynamic range (105-fold) in transcript abundances not previously observed with microarray technology. We discovered that transcripts for isoferritins and cathepsins are strikingly abundant during colostrum production, highlighting the potential importance of these proteins for neonatal health. Two transcripts, encoding β-casein (CSN2) and a-lactalbumin (LALBA), make up 45% of the total pool of mRNA in mature lactation. Genes significantly expressed across all stages of lactation are associated with making, modifying, transporting, and packaging milk proteins. Stage-specific transcripts are associated with immune defense during the colostral stage, up-regulation of the machinery needed for milk protein synthesis during the transitional stage, and the production of lipids during mature lactation. We observed strong modulation of key genes involved in lactose synthesis and insulin signaling. In particular, PTPRF may serve as a biomarker linking insulin resistance with insufficient milk supply. This study provides the methodology and reference data set to enable future targeted research on the physiological contributors to sub-optimal lactation in humans.
2013-07-22 | GSE45669 | GEO
Project description:Expression and differential expression analysis of milk samples from healthy and diseased diary cows. Diseases were grouped by their occurrence in the mammary gland or extra-mammary. Furthermore, the diseases were classified by their severity. All cows were examined thoroughly by the dairy herd manager, trained staff, or a veterinarian. Expression and differential expression was assessed by using the Affymetrix Bovine Genome Array (GPL2112). Control animals (2-4 years old, 1st to 3th lactation, one animal 4th and one 8th lactation) showed no clinical signs of disease and had no abnormalities in the udder or milk. Their somatic cell count (SCC) was less than 100,000 cells/ml milk. Most of the control samples were taken during early lactation (10-100 days post-partum, dpp). Diseased cows were in their 1st to 8th lactation within 10-220 dpp.
2018-06-29 | GSE93082 | GEO
Project description:Milk contains microRNAs (miRNAs) that are protected by extracellular vesicles (EV). Beyond variations among individuals, the nutritional conditions of cattle play a role in shaping these milk miRNA profiles. This study explored milk-derived EV-miRNA variations induced by inulin supplementation and analyzed involved pathways. Fourteen lactating cows with sub-clinical mastitis were equally and randomly divided into an inulin and a control group. Cows in the inulin group received 300 g/d inulin, while the control group did not. After one week of adaptation and five weeks of treatment, milk-derived EV-miRNAs from cows were isolated. Differentially expressed (DE) miRNAs were identified via high-throughput sequencing. Functional enrichment analyses, including Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, were conducted to examine the target genes of DE miRNAs. Inulin supplementation did not significantly alter miRNA length, the number of known miRNAs, or the read number of small RNAs.
2024-05-31 | GSE256521 | GEO