Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1103402 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29232900_1.fastq.gz | Fastqsanger.gz | |||
| SRR29232900_2.fastq.gz | Fastqsanger.gz | |||
| SRR29232901_1.fastq.gz | Fastqsanger.gz | |||
| SRR29232901_2.fastq.gz | Fastqsanger.gz | |||
| SRR29232902_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcript profiling was performed by Affymetrix microarray analysis and SAGE to characterize changes in gene expression in the bovine mammary gland in response to 4× versus 2× daily milking during the first week of lactation. These changes in gene expression may contribute to the increased milk production observed in response to increased milking frequency. Our results indicate that increased milking frequency alters expression of genes in the mammary gland related to increased extracellular matrix remodeling, neovascularization, metabolism, cell proliferation and apoptosis. Keywords: Physiological response to stimulus
2007-12-23 | GSE9344 | 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
Project description:In a recent study, a teat disinfectant based on a nisin-producing Lactococcus cremoris displayed comparable efficacy to a conventional iodophor disinfectant in preventing dairy cow mastitis when implemented in the dairy cow milking routine. Here, we carried out a longitudinal study for an in-depth investigation of the milk proteome. Four groups of matched quarter milk with low and high somatic cell count (SCC) collected at the beginning (T0) and at the end (TF) of the trial were selected for analysis, for a total of 28 low SCC (LSCC) and 12 high SCC (HSCC) samples. The milk was delipidated, digested into peptides, and subjected to a proteomic analysis workflow entailing NanoHPLC separation and tandem mass spectrometry (LC-MS/MS) on an Orbitrap Fusion Tribrid mass spectrometer. The proteins were identified with MaxQuant, the proteomes were compared for identifying differential proteins, and their interaction networks were assessed with STRING. In LSCC milk at T0, 31 were increased or present only in the Lactococcus (L) disinfectant group (from now INCREASED in L) and 59 proteins were decreased in L disinfectant group or present only in the conventional iodophor (C) group (from now DECREASED in L). All were involved in metabolic pathways and were likely related to physiological differences between animals. In LSCC milk at TF, 34 proteins were INCREASED in L and 46 proteins were DECREASED in the L disinfectant group. Most belonged to physiological milk pathways, but 3 antimicrobial proteins were enriched in the L group at the end of the trial. In HSCC milk at T0, 54 proteins were INCREASED in L and 34 DECREASED in L. Most were involved in physiological metabolic pathways; 4 proteins with antimicrobial functions were higher in L at the beginning of the trial. In HSCC milk at TF, 67 proteins were INCREASED in L and 39 DECREASED in L. All the proteins enriched in C belonged to metabolic pathways, while up to 14 proteins enriched in L were involved in antibiotic, antimicrobial, and immune defense pathways. Cathelicidins were among the most prominent differential proteins with antimicrobial functions. At T0, cathelicidins were generally higher in HSCC than LSCC milk of both experimental groups, as expected. At TF, they were increased or unique only in the Lactococcus group, in both LSCC and HSCC milk. Western immunoblotting validation confirmed the proteomic findings. On the other hand, enzymatic assessment of n-acetyl-glucosaminidase (NAGase) did not highlight significant differences between the C and L groups, neither for LSCC nor for HSCC milk. In conclusion, the two disinfectants did not induce relevant functional changes in the milk proteome of healthy animals, except for three increased antimicrobial proteins in the Lactococcus group. On the other hand, in animals with an underlying mammary gland inflammation, the milk proteome of the Lactococcus group showed increased levels of several proteins with antibiotic, antimicrobial and immune defense functions. Among other factors, the selective immunostimulatory action of nisin, the antimicrobial effector of L. cremoris, might play a role in this observation.
2024-10-17 | PXD045030 | Pride
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:Given that different diets could alter cow milk yield and composition, the effects of different feed formula on milk extracellular vesicle (EV) miRNAs were detected. Cow milk EVs contained various small RNAs, including miRNAs, snRNAs, tiRNAs, Cis-regulatory elements, and piRNAs. Two hundred and seventy-six known bos taurus miRNAs were identified by sequencing in bovine milk EVs. There were 13 immune-related miRNAs in the top 20 miRNAs in milk EVs. Nine differently expressed known miRNAs were detected in responding to different feed formulations. Cow milk EVs are abundant of small RNAs, especially miRNAs, which might be closely related to the development of maternal mammary gland and neonatal immune maturity.
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Project description:We investigated miRNA expression in Holstein dairy cow of mammary gland with different producing quality milk using high-throughput sequence and qRT-PCR techniques. miRNA libraries were constructed from mammary gland tissues taken from a high producing quality milk and a low producing quality milk Holstein dairy cow, the small RNA digitalization analysis based on HiSeq high-throughput sequencing takes the SBS-sequencing by synthesis.The libraries included 4732 miRNAs. A total of 124 miRNAs in the high producing quality milk mammary gland showed significant differences in expression compared to low producing quality milk mammary gland (P<0.05). Conclusion: Our study provides a broad view of the bovine mammary gland small RNA expression profile characteristics. Differences in types and expression levels of miRNAs were observed between high producing quality milk and a low producing quality milk Holstein dairy cow
2016-12-31 | GSE57991 | 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