Expression and differential expression analysis of milk samples from healthy and diseased diary cows.
Ontology highlight
ABSTRACT:
ORGANISM(S): Bos taurus
PROVIDER: GSE93082 | GEO | 2018/06/29
REPOSITORIES: GEO
Similar Datasets
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:The aim of this study was to determine the effects of linseed dietary supplementation on gene expression in the mammary gland of grazing dairy cows. Milk composition and gene expression in the mammary gland tissue were evaluated in dairy cows supplemented with linseed. The linseed supplementation improves the health and nutrition quality aspects of dairy milk, but also affects the gene networks expression signature associated with cellular growth and proliferation, cell-death, signalling, nutrient metabolism, and immune response, and in turn, the mammary gland integrity and health. The experiment was carried out in a complete randomized blocked designed structure comprising 14 Holstein-Friesian cows (6 second parity, 2 third parity and 6 older cows), selected from a 550-cow herd. Cows were paired in 7 blocks on the basis of similarity in parity (second parity, third parity and older cows), expected date of calving, and milk performance in the previous lactation (in order of priority). Cows within each block were randomly allocated to one of two treatment groups, “Omega” or “Control”. The dietary Omega treatment consisted of a basal diet supplemented with a concentrate-mixture including linseed on a dry matter (DM) basis, whereas cows in treatment group Control were supplemented with a concentrate mixture without linseed. Linseed was chosen because it is rich in c9,c12,c15-18:3 (ALA). Concentrate mixtures were fed with a concentrate dispenser. Experimental treatments started 3 weeks before the expected calving date (wk -3) and lasted until 6 weeks after calving (wk 6).
2012-11-18 | E-GEOD-24200 | biostudies-arrayexpress
Project description:Milk protein is one of the most important economic traits in the dairy industry. Yet, the miRNA gene regulatory network for the synthesis of milk protein in mammary is poorly understood. In this study, the hypothesis was that miRNAs have potential roles in bovine milk protein production. Using miRNA-seq and RNA-seq, we investigated the miRNAs profiles of mammary glands from 12 Chinese Holstein cows with six cows at peak of lactation and six in non-lactating period, from which three cows were in high and three in low milk protein percentage.
2021-08-11 | GSE181766 | GEO
Project description:BACKGROUND: The lactating mammary gland responds to changes in milking frequency by modulating milk production. This response is locally regulated and, in dairy cows, the udder is particularly sensitive during early lactation. Relative to cows milked twice-daily throughout lactation, those milked four-times-daily for just the first 3 weeks of lactation produce more milk throughout that lactation. We hypothesized that the milk yield response would be associated with increased mammary cell turnover and changes in gene expression during frequent milking and persisting thereafter. Cows were assigned to unilateral frequent milking (UFM; left udder halves milked twice-daily; right udder halves milked four-times daily) on days 1 to 21 of lactation, followed by twice-daily milking for the remainder of lactation. Relative to udder halves milked twice-daily, those milked four-times produced more milk during UFM; the difference in milk yield declined acutely upon cessation of UFM after day 21, but remained significantly elevated thereafter. We obtained mammary biopsies from both udder halves on days 21, 23, and 40 of lactation. RESULTS: Mammary cell proliferation and apoptosis were not affected by milking frequency. We identified 75 genes that were differentially expressed between paired udder halves on day 21 but exhibited a reversal of differential expression on day 23. Among those genes, we identified four clusters characterized by similar temporal patterns of differential expression. Two clusters (11 genes) were positively correlated with changes in milk yield and were differentially expressed on day 21 of lactation only, indicating involvement in the initial milk yield response. Two other clusters (64 genes) were negatively correlated with changes in milk yield. Twenty-nine of the 75 genes were also differentially expressed on day 40 of lactation. CONCLUSIONS: Changes in milking frequency during early lactation did not alter mammary cell population dynamics, but were associated with coordinated changes in mammary expression of at least 75 genes. Twenty-nine of those genes were differentially expressed 19 days after cessation of treatment, implicating them in the persistent milk yield response. We conclude that we have identified a novel transcriptional signature that may mediate the adaptive response to changes in milking frequency.
2014-01-01 | GSE27851 | 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 GeneChipM-BM-. 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 M-bM-^IM-$ 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. 8 samples from 4 cows in experiment 1; 6 samples from 3 cows in experiment 2
2012-02-27 | E-GEOD-27380 | biostudies-arrayexpress
Project description:Bovine mammary gland provide the largest amount of milk for dairy industry to date. Insight in functional adaptation of this organ is critical in order to improve efficiency of milk synthesis and milk quality. In the present experiment microarray analysis in combination with bioinformatics tools was performed in mammary tissue from 8 Holstein cows during the entire lactation cycle.
2012-03-01 | GSE19055 | GEO
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: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
Project description:Four-times daily milking during the first 3 weeks of lactation elicits an increase in milk yield, which persists through late lactation even after twice-daily milking is imposed. We hypothesized that this milk yield response would be associated with changes in mammary proliferation, apoptosis, and gene expression, which would persist throughout lactation. Six multiparous cows were assigned to unilateral frequent milking (UFM; twice daily milking of the left udder half (2X), four-times daily milking of the right udder half (4X)) on days 1 to 21 of lactation, followed by 2X thereafter. Udder halves initially milked 4X produced more milk than those milked 2X during, and after UFM treatment, through 180 days in milk (DIM). To determine the mechanisms involved in the persistent milk yield response, we obtained mammary biopsies from both udder halves at 21, 23, and 40 DIM. Rates of [3H]-thymidine incorporation into DNA in vitro and mammary cell apoptosis were not affected by UFM or DIM. Using Affymetrix GeneChipM-BM-. Bovine Genome Arrays, we determined that the differential expression (4X vs. 2X) of 18 genes was significantly affected by DIM. Within the group of 18 differentially expressed genes, we identified a cluster of 15 genes with a similar temporal pattern of differential expression. Nine of the genes in the cluster remained differentially expressed at 40 DIM, indicating that they may be involved in the persistent milk yield response. Among the genes in the cluster were chitinase 3-like (CHI3L)-1, clusterin, early growth response (EGR)-1, and sex determining region Y-box (SOX)-4. These genes have been associated with mammary development, differentiation and remodeling; all of which may be functionally related to the increase in milk yield. We conclude that frequent milking during early lactation does not alter mammary growth but is associated with changes in mammary expression of 18 genes. Future experiments will determine the function of these genes in the mammary gland, and will clarify their role in the autocrine regulation of milk production and long-term alteration of mammary function. 36 samples from 6 cows; 3 timepoints
2014-01-01 | E-GEOD-27851 | biostudies-arrayexpress
Project description:Bovine mammary gland provide the largest amount of milk for dairy industry to date. Insight in functional adaptation of this organ is critical in order to improve efficiency of milk synthesis and milk quality. In the present experiment microarray analysis in combination with bioinformatics tools was performed in mammary tissue from 8 Holstein cows during the entire lactation cycle. The mammary biopsy was performed at -30, -15, 1, 15, 30, 60, 120, 240, and 300 days (d) relative to parturition. A dye-swap reference design (reference = mixture of RNA from several bovine tissues) was used.
2012-03-01 | E-GEOD-19055 | biostudies-arrayexpress