Temporal changes in bovine milk microbiota
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB47169 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR6558860_1.fastq.gz | Fastqsanger.gz | |||
| ERR6558860_2.fastq.gz | Fastqsanger.gz | |||
| ERR6558870_1.fastq.gz | Fastqsanger.gz | |||
| ERR6558870_2.fastq.gz | Fastqsanger.gz | |||
| ERR6558880_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 468 |
Similar Datasets
Project description:By comparison of the transcriptome profiles of udder quarters neighboring to infected quarters and healthy udder tissue we analyse gene expression in the late stage of infection with E. coli 1303. Differentially expressed genes and transcription factors regulating coexpressed genes identified by SOTA clustering were used to identify key genes that define systemic reactions to infection with E. coli 1303. Keywords: disease state analysis
2009-06-01 | GSE15022 | GEO
Project description:Mastitis, the inflammation of the mammary gland, is one of the most prevalent diseases in dairy farming worldwide. Unfortunately, the disease is most often present in a subclinical type with no clear symptoms. The sooner the infection is detected, the less opportunities for the disease to progress and the more treatment options remain available. Milk microRNA (miRNA) encapsulated in extracellular vesicles (EV) have been proposed as potential biomarkers of different mammary gland conditions, including subclinical mastitis. However, little is known about the robustness of EV analysis regarding sampling time-point or natural infections. In order to estimate the reliability of EV measurements in raw bovine milk, we first evaluated the changes in EV size, concentration and miRNA cargo during three consecutive days. Then, we compared milk EV differences from natural infected quarters with high somatic cell count (SCC) with their healthy adjacent quarters with low SCC and quarters from uninfected udders. We found that milk EV miRNA cargo is very stable along three days and that infected quarters do not induce relevant changes in milk EV of adjacent healthy quarters, making them suitable controls. We observed cow-individual changes in immunoregulatory miRNA in quarters with chronic subclinical mastitis, pointing towards infection-specific alterations. Finally, we proposed bta-miR-223 as a potential indicator of subclinical mastitis prognosis in raw milk.
2022-03-16 | GSE149856 | GEO
Project description:We hypothesized that accumulation of milk would influence gene expression in the mammary gland of lactating dairy cows. To test this hypothesis, we enrolled 4 multiparous Holstein cows (150 ± 10 DIM) in a half-udder milk stasis experiment. On day 1 of the experiment, cows were milked at 0430 h and at 1430 h, only right udder halves were milked. Mammary biopsies were obtained from both udder halves on day 2 of the experiment at 0500 h, immediately after right udder halves were milked and 12 h since left udder halves had last been milked. Using Affymetrix GeneChip® Bovine Genome Arrays, we identified 32 genes that were differentially expressed between left (full) and right (empty) udder halves (fold change > 1.5; P < 0.05). Four of the genes were downregulated in response to milk stasis, whereas 28 were upregulated. Differentially expressed genes were associated with extracellular matrix remodeling, tight junction formation, regulation of blood flow, and apoptosis. In addition, four of the differentially expressed genes had been previously identified as candidates for local regulation of milk production in dairy cows. Expression of two of these candidates, early growth response-1 (EGR-1) and thrombospondin-1 (THBS-1), was validated using real-time quantitative RT-PCR. Consistent with microarray results, both genes were upregulated in response to 24-h of milk stasis (P < 0.03). Immunofluorescence was used to localize expression of EGR-1 protein, which was restricted to epithelia and was uniformly distributed. We conclude that accumulation of milk alters gene expression in the bovine mammary gland. In particular, EGR-1 and THBS-1 have emerged as strong candidates for local regulation of milk production in dairy cows.
2014-01-01 | GSE27840 | GEO
Project description:By comparison of the transcriptome profiles of udder quarters neighboring to infected quarters and healthy udder tissue we analyse gene expression in the late stage of infection with E. coli 1303. Differentially expressed genes and transcription factors regulating coexpressed genes identified by SOTA clustering were used to identify key genes that define systemic reactions to infection with E. coli 1303. Experiment Overall Design: 10 samples, two conditions: udder quarters neighboring to one which was treated with E. coli for 24h vs healthy control * five replicates
2009-06-08 | E-GEOD-15022 | biostudies-arrayexpress
Project description:Host-microbiota interaction in bovine udder
| PRJEB54099 | ENA
Project description:We hypothesized that accumulation of milk would influence gene expression in the mammary gland of lactating dairy cows. To test this hypothesis, we enrolled 4 multiparous Holstein cows (150 M-BM-1 10 DIM) in a half-udder milk stasis experiment. On day 1 of the experiment, cows were milked at 0430 h and at 1430 h, only right udder halves were milked. Mammary biopsies were obtained from both udder halves on day 2 of the experiment at 0500 h, immediately after right udder halves were milked and 12 h since left udder halves had last been milked. Using Affymetrix GeneChipM-BM-. Bovine Genome Arrays, we identified 32 genes that were differentially expressed between left (full) and right (empty) udder halves (fold change > 1.5; P < 0.05). Four of the genes were downregulated in response to milk stasis, whereas 28 were upregulated. Differentially expressed genes were associated with extracellular matrix remodeling, tight junction formation, regulation of blood flow, and apoptosis. In addition, four of the differentially expressed genes had been previously identified as candidates for local regulation of milk production in dairy cows. Expression of two of these candidates, early growth response-1 (EGR-1) and thrombospondin-1 (THBS-1), was validated using real-time quantitative RT-PCR. Consistent with microarray results, both genes were upregulated in response to 24-h of milk stasis (P < 0.03). Immunofluorescence was used to localize expression of EGR-1 protein, which was restricted to epithelia and was uniformly distributed. We conclude that accumulation of milk alters gene expression in the bovine mammary gland. In particular, EGR-1 and THBS-1 have emerged as strong candidates for local regulation of milk production in dairy cows. 8 samples from 4 cows
2014-01-01 | E-GEOD-27840 | biostudies-arrayexpress
Project description:In this study we sought to establish changes within the mammary glands of lactating dairy cows (n=3-4) in response to a single dose of exogenous DEX by performing serial biopsies of alternating quarters of the udder Transcriptomic changes in the mammary glands in response to DEX were identified by RNA sequencing of mammary gland RNA at 0, 12, 24 and 72h post-DEX injection, followed by differential gene expression analysis Coincident with the milk yield and composition changes was the differential expression of 519 and 320 genes at 12 and 24 h after DEX, respectively, with return of all gene expression to baseline levels by 72 h.
2023-01-11 | GSE217369 | GEO
Project description:Regulation of milk synthesis and secretion is controlled mostly through local (intra-mammary) mechanisms. To gain insight into the molecular pathways comprising this response, an analysis of mammary gene expression was conducted in 12 lactating cows shifted from twice daily to once daily milking. Tissues were sampled by biopsy from adjacent mammary quarters of these animals during the two milking frequencies, allowing changes in gene expression to be assessed within each animal. Using bovine-specific, oligonucleotide arrays representing 21,495 unique transcripts, a range of differentially expressed genes were found as a result of less frequent milk removal.
2009-07-01 | GSE16876 | GEO
Project description:Milking dairy cows four times daily (4X) instead of twice daily (2X) during early lactation stimulates an increase in milk yield that partly persists through late lactation; however, the mechanisms behind this response are unknown. We hypothesized that the acute mammary response to regular milkings would be transient and would involve different genes from those that may be specifically regulated in response to 4X. Nine multiparous cows were assigned at parturition to unilateral frequent milking (UFM; 2X of the left udder half, 4X of the right udder half). Mammary biopsies were obtained from both rear quarters at 5 days in milk (DIM), immediately after 4X glands had been milked (Experiment 1; n = 4 cows), or 2.5 h after both udder halves had last been milked (Experiment 2; n = 5 cows). Affymetrix GeneChip® Bovine Genome Arrays were used to measure gene expression. Eight hundred and fifty five genes were differentially expressed in mammary tissue between 2X vs. 4X glands of cows in experiment 1 (FDR ≤ 0.05), whereas none were differentially expressed in experiment 2 using the same criterion. We conclude that there is an acute transcriptional response to milk removal, but 4X milking did not elicit differential expression of unique genes. Therefore, there does not appear to be a sustained transcriptional response to 4X milking on day 5 of lactation. Using a differential expression plot of data from both experiments, as well as qRT-PCR, we identified at least two genes that may be responsive to both milk removal and to 4X milking. Therefore, the milk yield response to 4X milking may be mediated by genes that are acutely regulated by removal of milk from the mammary gland.
2012-02-27 | GSE27380 | GEO