Ontology highlight
ABSTRACT:
PROVIDER: PRJNA699394 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13684565_1.fastq.gz | Fastqsanger.gz | |||
| SRR13684565_2.fastq.gz | Fastqsanger.gz | |||
| SRR13684566.fastq.gz | Fastqsanger.gz | |||
| SRR13684566_1.fastq.gz | Fastqsanger.gz | |||
| SRR13684566_2.fastq.gz | Fastqsanger.gz |
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Project description:The molecular processes underlying human milk production and the effects of mastitic infection are largely unknown because of limitations in obtaining tissue samples. Determination of gene expression in normal lactating women would be a significant step towards understanding why some women display poor lactation outcomes. Here we demonstrate the utility of RNA obtained directly from human milk cells to detect mammary epithelial cell (MEC)-specific gene expression. Milk cell RNA was collected from 5 time points (24 hours pre-partum during the colostrum period, mid lactation, two involution, and during a bout of mastitis) in addition to an involution series comprising three time points. Gene expression profiles were determined by use of human Affymetrix arrays. Milk cells collected during milk production showed that the most highly expressed genes were involved in milk synthesis (eg. CEL, OLAH, FOLR1, BTN1A1, ARG2), while milk cells collected during involution showed a significant down regulation of milk synthesis genes and activation of involution associated genes (eg. STAT3, NF-kB, IRF5, IRF7). Milk cells collected during mastitic infection revealed regulation of a unique set of genes specific to this disease state, whilst maintaining regulation of milk synthesis genes. Use of conventional epithelial cell markers was used to determine the population of MECâ??s within each sample. This paper is the first to describe the milk cell transcriptome across the human lactation cycle and during mastitic infection, providing valuable insight into gene expression of the human mammary gland. Human milk sampling throughout lactation cycle and during mastitic infection.
2016-04-01 | E-GEOD-77978 | biostudies-arrayexpress
Project description:Mastitis is a very costly and common disease in the dairy industry. The study of the transcriptome from healthy and mastitic milk somatic cell samples using RNA-Sequencing technology (RNA-Seq) can provide measurements of transcript levels associated with the immune response to the infection. The objective of this study was to characterize the Holstein milk somatic cells transcriptome from 6 cows to determine host response to intramammary infections. RNA-Sequencing was performed on two samples from each cow from two separate quarters, one classified as healthy (n = 6) and one as mastitic (n = 6). In total, 449 genes were differentially expressed between the healthy and mastitic quarters (P-value < 0.01, FDR < 0.05, FC > ±2). Among the differentially expressed genes, the most expressed genes based on Reads Per Kilo base per Million mapped reads (RPKM) in the healthy group were associated with milk components (CSN2 and CSN3), and in the mastitic group they were associated with immunity (B2M and CD74). In-silico functional analysis was performed using the list of 449 differentially expressed genes, which identified 36 significantly enriched metabolic pathways (FDR < 0.01), some of which were associated with the immune system, such as cytokine-cytokine interaction and cell adhesion molecules. Seven functional candidate genes were selected, based on the criteria of being highly expressed and present in significant pathways that are relevant to the inflammatory process (GLYCAM1, B2M, CD74, BoLA DR-Alpha, FCER1G, SDS and NFKBIA). Lastly, we identified the differentially expressed genes that are located in QTL regions previously known to be associated with mastitis, specifically clinical mastitis, somatic cell count and somatic cell score. It was concluded that there are multiple genes within QTL regions that could potentially impact host response to mastitis causing agents, making some cows more susceptible to intramammary infections. The identification of key genes with functional, statistical, biological and positional relevance associated with host defense to infection, will contribute to a better understanding of the underlying genetic architecture associated with mastitis. This in turn will improve the sustainability of agricultural practices, by facilitating the selection of cows with improved host defense leading to increased resistance to mastitis.
2019-10-22 | GSE131607 | GEO
Project description:The molecular processes underlying human milk production and the effects of mastitic infection are largely unknown because of limitations in obtaining tissue samples. Determination of gene expression in normal lactating women would be a significant step towards understanding why some women display poor lactation outcomes. Here we demonstrate the utility of RNA obtained directly from human milk cells to detect mammary epithelial cell (MEC)-specific gene expression. Milk cell RNA was collected from 5 time points (24 hours pre-partum during the colostrum period, mid lactation, two involution, and during a bout of mastitis) in addition to an involution series comprising three time points. Gene expression profiles were determined by use of human Affymetrix arrays. Milk cells collected during milk production showed that the most highly expressed genes were involved in milk synthesis (eg. CEL, OLAH, FOLR1, BTN1A1, ARG2), while milk cells collected during involution showed a significant down regulation of milk synthesis genes and activation of involution associated genes (eg. STAT3, NF-kB, IRF5, IRF7). Milk cells collected during mastitic infection revealed regulation of a unique set of genes specific to this disease state, whilst maintaining regulation of milk synthesis genes. Use of conventional epithelial cell markers was used to determine the population of MEC’s within each sample. This paper is the first to describe the milk cell transcriptome across the human lactation cycle and during mastitic infection, providing valuable insight into gene expression of the human mammary gland.
2016-04-01 | GSE77978 | GEO
Project description:Milk microRNAs (miRNAs) encapsulated in extracellular vesicles (EVs) are a novel class of bioactive food compounds. Milk produced by cows with subclinical mastitis threatens animals healthy and milk safety. However, little is known about the differentially expressed miRNA in milk-derived EVs related to subclinical mastitis. This study profiled miRNAs in milk-derived EVs from healthy cows and cows with subclinical mastitis. The potential targets for differentially expressed (DE) miRNAs were predicted. Milk-derived EVs were isolated from healthy cows (n = 7, the control group) and cows with subclinical (n = 7, the SM group). Two hundred ninety miRNAs (221 known and 69 novel ones) were identified. The top 20 miRNAs were commonly abundant (> 0.1% of the total read counts) in Healthy and SM groups, were regarded as abundant bovine milk-derived EVs miRNAs. MiR-21-5p was the most highly expressed known miRNA. Target genes of the top 20 abundant miRNAs were significantly enriched in Ras signaling pathway. The bta-miR-21-5p, bta-miR-30a-5p and miR-6-1096 were differentially expressed. For DE miRNAs, there was no significantly enriched pathways were found in the KEGG enrichment analysis. The linkage between the validated target genes and diseases suggested that we pay particular attention to exosome miRNAs from mastitic milk in milk safety.
2022-08-31 | GSE201588 | GEO
Project description:Previous studies have investigated the peptidomic changes occurring in cow milk during mastitis; however, these focused mainly on clinical mastitis, either spontaneous (Mansor et al., 2013) or induced by experimental infection (Thomas et al., 2016). Mansor and coworkers were the first to use mass spectrometry to demonstrate that several peptides found increased in milk from cows with clinical S. aureus or E. coli mastitis were mainly derived from aS1- and b-casein. In that study, 48 peptides were significantly different between the milks of healthy and mastitic cows. Non-mastitic samples were confirmed to be non-mastitic by having SCC <100,000 cells/mL (Mansor et al., 2013). Thomas and coworkers expanded the peptidomic repertoire in a study evaluating the kinetics of experimental S. uberis infection, and found signature peptides with potential as mastitis markers (Thomas et al., 2016). Only one study evaluated the milk peptidome in subclinical mastitis (Guerrero et al., 2015) demonstrating that even subclinical infections can cause significant increases in the total number of released peptides when compared to uninfected milk. However, neither the IMI agents nor the somatic cell counts were reported. With the aim of understanding high abundance protein and peptidomic changes due to subclinical CNS mastitis, to identify signature peptides with potential for subclinical mastitis detection, and to compare the proteomic and peptidomic findings with those reported in clinical mastitis, we investigated the influence of CNS IMI on high abundance milk proteins by SDS-PAGE and densitometric analysis, followed by a detailed characterization of the milk peptidome by means of high-performance liquid chromatography/tandem mass spectrometry and bioinformatic analysis.
2020-07-15 | PXD017768 | Pride
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:Comparative transcriptome analysis between six adipose depots in buffaloes
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