MiRNA expression profiles of early lactation and early involution in dairy goat mammary gland tissues
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ABSTRACT:
ORGANISM(S): Capra hircus
PROVIDER: GSE79692 | GEO | 2017/12/31
SECONDARY ACCESSION(S): PRJNA316716
REPOSITORIES: GEO
Similar Datasets
Project description:Lactogenesis includes two stages. Stage â
begins a few weeks before parturition, and stage â
¡ begins a few weeks before parturition. In order to better understand the molecular events driving lactogenesis in dairy cows, genome-wide gene expression profiling was conducted using digital gene expression profiling (DGE) on bovine mammary tissue at three time points (on approximately day 35 before parturition (-35d), day 7 before parturition (-7d) and day 3 after parturition (+3d)). Approximately 6.2 million, 5.8 million and 6.1 million 21-nt cDNA tags were sequenced in the three cDNA libraries (-35d, -7d and +3d), respectively. After aligning to the reference sequences, the three cDNA libraries included 8,662, 8,363 and 8,359 genes, respectively. With a fold change cutoff criteria of â¥2 or â¤-2 and a false discovery rate (FDR) of â¤0.001, a total of 812 genes were significantly differentially expressed at -7d compared with -35d (stage â
). There were 234 genes upregulated and 578 genes downregulated, accounting for 28.8ï¼
and 71.2ï¼
of differentially expressed genes respectively. A total of 1,189 genes were significantly differentially expressed at +3d compared with -7d (stag â
¡). Of these genes with significant expression changes, 274 (23.0ï¼
) genes were upregulated. 915 (77.0ï¼
) genes were downregulated. The results suggest that the mammary gland begins to lactate not only by a gain of function but also by a broad suppression of function to effectively push most of the cellï¼s resources towards lactation. Examination of genome-wide gene expression profiling using digital gene expression profiling (DGE) on bovine mammary tissue at three time points of approximately day 35 before parturition, day 7 before parturition and day 3 after parturition. There were 6 cows in each group. The mammary tissue from cows in the same group were pooled together for RNA isolation. The total RNA was used to sequence.
2016-03-01 | E-GEOD-44796 | biostudies-arrayexpress
Project description:Lactogenesis includes two stages. Stage Ⅰ begins a few weeks before parturition, and stage Ⅱ begins a few weeks before parturition. In order to better understand the molecular events driving lactogenesis in dairy cows, genome-wide gene expression profiling was conducted using digital gene expression profiling (DGE) on bovine mammary tissue at three time points (on approximately day 35 before parturition (-35d), day 7 before parturition (-7d) and day 3 after parturition (+3d)). Approximately 6.2 million, 5.8 million and 6.1 million 21-nt cDNA tags were sequenced in the three cDNA libraries (-35d, -7d and +3d), respectively. After aligning to the reference sequences, the three cDNA libraries included 8,662, 8,363 and 8,359 genes, respectively. With a fold change cutoff criteria of ≥2 or ≤-2 and a false discovery rate (FDR) of ≤0.001, a total of 812 genes were significantly differentially expressed at -7d compared with -35d (stage Ⅰ). There were 234 genes upregulated and 578 genes downregulated, accounting for 28.8％ and 71.2％ of differentially expressed genes respectively. A total of 1,189 genes were significantly differentially expressed at +3d compared with -7d (stag Ⅱ). Of these genes with significant expression changes, 274 (23.0％) genes were upregulated. 915 (77.0％) genes were downregulated. The results suggest that the mammary gland begins to lactate not only by a gain of function but also by a broad suppression of function to effectively push most of the cell＇s resources towards lactation.
2016-03-01 | GSE44796 | 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: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:Cows exposed to short day photoperiod (SD, 8L:16D) during the 60-day non-lactating period prior to parturition produce more milk in their subsequent lactation compared to cows exposed to long day photoperiod (LD,16L:8D). Although this response is well-established in dairy cows, the underlying mechanisms are not understood. We hypothesized that differential gene expression in cows exposed to SD or LD photoperiods during the dry period could be used to identify the functional basis for the subsequent increase in milk production during lactation. Pregnant, multiparous cows were maintained on a SD or LD photoperiod for 60-days prior to parturition. Mammary biopsies were obtained on days -24 and -9 relative to parturition and Affymetrix GeneChip® Bovine Genome Arrays were used to quantify gene expression. Sixty-four genes were differentially expressed (p ≤ 0.05 and fold-change ≥ |1.5|) between SD and LD treatments. Many of these genes were associated with cell growth and proliferation, or immune function. Ingenuity Pathway Analysis predicted upstream regulators to include TNF, TGFβ1, interferon γ and several interleukins. In addition, expression of 125 genes was significantly different between day -24 and day -9; those genes were associated with milk component metabolism and immune function. The interaction of photoperiod and time affected 32 genes associated with insulin-like growth factor (IGF-I) signaling. Genes differentially expressed in response to photoperiod were associated with mammary development and immune function consistent with the enhancement of milk yield in the ensuing lactation. Our results provide insight into the mechanisms by which photoperiod affects the mammary gland and subsequently lactation. Data were analyzed for the effect of photoperiod treatment (LD minus SD), time relative to parturition (day -24 minus day -9) and the interaction of photoperiod treatment and time ((LD minus SD day -9) minus (LD minus SD day -24))
2015-09-01 | GSE65059 | 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 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: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:Dynamic transcriptome profiles in yak mammary gland were evaluated by sampling mammary tissue at -30, -15, 1, 15, 30, 60, 120, 180 and 240 d relative to parturition and using a bovine commercial microarray platform. Several bioinformatics tools were used to analyze the data, both as expression relative to -30 d and as expression relative to the previous time point. There were >6,000 differentially expressed transcript (DEG; FDR＜0.05; P＜0.05) throughout lactation with larger DEG observed at the onset (1 vs. -15d) and at the end of lactation (240 vs. 180d). Bioinformatics analysis allowed to identify lactation-related genes on yak chromosomes which laid the foundation for determination of QTL location. Among most-impacted bovine chromosomes (BTA), BTA6, BTA9 and BTA28 were induced while BTA3, BTA4 and BTA14 were inhibited throughout lactation. Functional analysis underlined an overall induction of lipid metabolism, suggesting increases in triglycerides synthesis likely regulated by PPAR signaling. Data suggested induction of amino acid metabolism while increasing secretion or protein, but decreasing proteasome, indicating a major role of amino acid handling and reduced protein degradation in the synthesis and secretion of milk proteins. Glycan biosynthesis, both for N-glycan and O-glycan, was induced suggesting increased glycan content in milk. Cell cycle and immune response, especially antigen processing and presentation, were strongly inhibited during lactation suggesting morphological changes were minimized while the mammary gland prevents immune hyper responses during lactation. Transcripts associated with response to radiation and low oxygen were enriched in the down-regulated DEG affected by stage of lactation. Except for the latter, functions affected by the transcriptomic adaptation to lactation in mammary tissue of yak were very similar to the ones observed in dairy cows.
2022-04-28 | GSE201438 | GEO
Project description:The objective of this study was to apply a quantitative proteomic approach to investigate changes in the plasma proteome of normal and over-conditioned dairy cows during the transition period. We used an animal model with a targeted difference in body condition score (BCS) at calving. For this, multiparous Holstein cows were allocated to two groups 15 weeks before anticipated calving and were fed differently to reach either high (HBCS: 7.2 NEL MJ/kg dry matter (DM) or normal BCS (NBCS: 6.8 NEL MJ/kg DM) until dry-off. Thereafter, both groups were fed identical diets. The targeted BCS difference was sustained during the dry period (7 weeks before calving) and the subsequent 12 weeks of lactation. Plasma samples (n = 5) from d -49, +7, and +21 relative to parturition were used from both groups (each n = 5) for proteome profiling in aby applying quantitative Tandem Mass Tags (TMT) approach.
2020-04-16 | PXD015958 | Pride
Project description:The transition between pregnancy and lactation is a major physiological change that dairy cows must contend with. Complex systemic and local processes involving gluconeogenesis, energy balance, utilisation of body reserves, insulin resistance and involution of the uterus can have an effect on animal health and farm profitability. Here we used an established Holstein cow model of fertility that displayed genetic and phenotypic divergence in calving interval, a trait used to define reproductive performance using a national breeding index in Ireland. Cows had similar genetic merit for milk production traits, but either very good genetic merit for fertility (‘Fert+’; n = 8) or very poor genetic merit for fertility (‘Fert-‘; n = 8). We investigated three distinct time-points, late pregnancy, early lactation and mid lactation (-18, 1 and 147 days on average with day 0 being birth), using RNA sequencing from both liver and muscle tissue biopsies and conducting a differential expression (DE) analysis. We found 807 and 815 unique genes to be DE in at least one time-point in liver and muscle respectively, of which 79% and 83% were only found in a single time-point; 40 and 41 genes were found DE at every time-point indicating possibly systemic or chronic dysregulation. Functional annotation resulted in evidence for two major physiological processes: immune and inflammation, and metabolic, lipid and carbohydrate-binding. These processes indicate areas of previous interest as well as specific systems that appear differentially regulated, and point towards interesting avenues of further research in a broad and complex field.
2015-10-08 | GSE62159 | GEO