MiRNA expression data from post-partum dairy cattle (Holstein Friesian) liver
Ontology highlight
ABSTRACT:
ORGANISM(S): Bos taurus
SUBMITTER: Dermot Morris
PROVIDER: E-GEOD-51658 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:High yielding dairy cattle undergo a state of NEB (negative energy balance) during the post-partum period when energy demand for lactation and maintenance exceeds energy intake. During this period in order to counteract NEB the liver under goes extensive metabolic and physiological change resulting in alteration in hepatic genes and miRNAs expression. We used Affymetrix Multispecies miRNA-2_0 Array with miRBase version 15 coverage to assess the liver miRNA expression in SNEB (severe NEB) and MNEB (mild NEB) Holstein Friesian cattle during the post-partum period.
2013-10-25 | GSE51658 | GEO
Project description:Background: The liver is central to most economically important metabolic processes in cattle. However, the changes in expression of genes that drive these processes remain incompletely characterised. RNA-seq is the new gold standard for whole transcriptome analysis but so far there are no reports of its application to analysis of differential gene expression in cattle liver. We used RNA-seq to study differences in expression profiles of hepatic genes and their associated pathways in individual cattle in either mild negative energy balance (MNEB) or severe negative energy balance (SNEB). NEB is an imbalance between energy intake and energy requirements for lactation and body maintenance. This aberrant metabolic state affects high-yielding dairy cows after calving and is of considerable economic importance because of its negative impact on fertility and health in dairy herds. Analysis of changes in hepatic gene expression in SNEB animals will increase our understanding of NEB and contribute to the development of strategies to circumvent it. Results: RNA-seq analysis was carried out on total RNA from liver from early post partum Holstein Friesian cows in MNEB (n=5) and SNEB (n=6). 12,833 genes were deemed to be expressed (>4 reads per gene per animal), 413 of which were shown to be statistically significantly differentially expressed (SDE) at a false discovery rate (FDR) of 0.1% and 200 of which were SDE (FDR of 0.1%) with a ≥2-fold change between MNEB and SNEB animals. GOseq/KEGG pathway analysis showed that SDE genes with ≥2- fold change were associated (P <0.05) with 9 KEGG pathways. Seven of these pathways were related to fatty acid metabolism and unexpectedly included ‘Steroid hormone biosynthesis’, a process which mainly occurs in the reproductive organs rather than the liver. Conclusions: RNA-seq analysis showed that the major changes at the level of transcription in the liver of SNEB cows were related to fat metabolism. 'Steroid hormone biosynthesis', a process that normally occurs in reproductive tissue, was significantly associated with changes in gene expression in the liver of SNEB cows. Changes in gene expression were found in this pathway that have not been previously been identified in SNEB cows. 11 liver RNA samples were analysed in total, 6 samples were from SNEB animals and 5 samples from MNEB animals
2012-04-25 | E-GEOD-37544 | biostudies-arrayexpress
Project description:Background: The liver is central to most economically important metabolic processes in cattle. However, the changes in expression of genes that drive these processes remain incompletely characterised. RNA-seq is the new gold standard for whole transcriptome analysis but so far there are no reports of its application to analysis of differential gene expression in cattle liver. We used RNA-seq to study differences in expression profiles of hepatic genes and their associated pathways in individual cattle in either mild negative energy balance (MNEB) or severe negative energy balance (SNEB). NEB is an imbalance between energy intake and energy requirements for lactation and body maintenance. This aberrant metabolic state affects high-yielding dairy cows after calving and is of considerable economic importance because of its negative impact on fertility and health in dairy herds. Analysis of changes in hepatic gene expression in SNEB animals will increase our understanding of NEB and contribute to the development of strategies to circumvent it. Results: RNA-seq analysis was carried out on total RNA from liver from early post partum Holstein Friesian cows in MNEB (n=5) and SNEB (n=6). 12,833 genes were deemed to be expressed (>4 reads per gene per animal), 413 of which were shown to be statistically significantly differentially expressed (SDE) at a false discovery rate (FDR) of 0.1% and 200 of which were SDE (FDR of 0.1%) with a ≥2-fold change between MNEB and SNEB animals. GOseq/KEGG pathway analysis showed that SDE genes with ≥2- fold change were associated (P <0.05) with 9 KEGG pathways. Seven of these pathways were related to fatty acid metabolism and unexpectedly included ‘Steroid hormone biosynthesis’, a process which mainly occurs in the reproductive organs rather than the liver. Conclusions: RNA-seq analysis showed that the major changes at the level of transcription in the liver of SNEB cows were related to fat metabolism. 'Steroid hormone biosynthesis', a process that normally occurs in reproductive tissue, was significantly associated with changes in gene expression in the liver of SNEB cows. Changes in gene expression were found in this pathway that have not been previously been identified in SNEB cows.
2012-04-25 | GSE37544 | GEO
Project description:Most dairy cows suffer uterine microbial contamination postpartum. Persistent endometritis often develops, associated with reduced fertility. We used a model of differential feeding and milking regimes to produce cows in differing negative energy balance (NEB) status in early lactation. We used Affymetrix GeneChipM-CM-^R Bovine Genome Array to investigate the global gene expression underlying negative energy balance and to identify the significantly differentially expressed genes during this process. We investigate the differences of gene expression profiles in uterine endometrial tissues between the cows with mild and severe negative energy balance.
2009-04-04 | E-GEOD-15544 | biostudies-arrayexpress
Project description:Negative energy balance (NEB) is an altered metabolic state in high yielding cows that occurs during the first few weeks postpartum when energy demands for lactation and maintenance exceed the energy supply from dietary intake. NEB can, in turn, lead to metabolic disorders and to reduced fertility. Alterations in the expression of more than 700 hepatic genes have previously been reported in a study of NEB in postpartum dairy cows. miRNAs (microRNA) are known to mediate many alterations in gene expression post transcriptionally. To study the hepatic miRNA content of postpartum dairy cows, including their overall abundance and differential expression, in mild NEB (MNEB) and severe NEB (SNEB) short read RNA sequencing was carried out. A NEB dairy cow model developed previously was used. In this model differential feeding and milking regimes were used to produce two groups of Holstein Friesian cows; MNEB and SNEB. Briefly, MNEB cows were fed ad libitum grass silage with 8 kg/day of a 21% crude protein dairy concentrate and milked once daily. SNEB cows were fed 25 kg/day silage with 4 kg/day concentrate and milked thrice daily. All procedures were carried out under license in accordance with the European Community Directive, 86-609-EC. Cows were slaughtered approximately 14 days postpartum (MNEB; 13.6 ± 0.75, range 11–15; SNEB 14.3 ± 0.56, range 13–16 ) and the entire liver was removed within 15 to 30 min. Samples weighing approximately 1 g were dissected, rinsed in RNase-free phosphate buffer, snap-frozen in liquid nitrogen and stored at -80ºC. Liver tissue samples from 5 SNEB and 3 MNEB animals were used for miRNA library preparation.
2014-03-14 | E-GEOD-55882 | biostudies-arrayexpress
Project description:Increased energy demands to support lactation, coupled with lowered feed intake capacity results in negative energy balance (NEB) and is typically characterized by extensive mobilization of body energy reserves in the early postpartum dairy cow. The catabolism of stored lipid leads to an increase in the systemic concentrations of nonesterified fatty acids (NEFA) and -hydroxy butyrate (BHB). Oxidation of NEFA in the liver result in the increased production of reactive oxygen species and the onset of oxidative stress and can lead to disruption of normal metabolism and physiology. The immune system is depressed in the peripartum period and early lactation and dairy cows are therefore more vulnerable to bacterial infections causing mastitis and or endometritis at this time. A bovine Affymetrix oligonucleotide array was used to determine global gene expression in the spleen of dairy cows in the early postpartum period. Spleen tissue was removed post mortem from five severe NEB (SNEB) and five medium NEB (MNEB) cows 15 days postpartum.SNEB increased systemic concentrations of NEFA and BHB, and white blood cell and lymphocyte numbers were decreased in SNEB animals. A total of 545 genes were altered by SNEB. Network analysis using Ingenuity Pathway Analysis revealed that SNEB was associated with NRF2-mediated oxidative stress, mitochondrial dysfunction, endoplasmic reticulum stress, natural killer cell signaling, p53 signaling, downregulation of IL-15, BCL-2, and IFN- ; upregulation of BAX and CHOP and increased apoptosis with a potential negative impact on innate and adaptive immunity. Multiparous Holstein-Friesian cows (n=24) were blocked 2 weeks prior to expected calving date according to parity, body condition score, and previous lactation yield (average lactation 6477M-BM-1354kg) and randomly allocated to mild (MNEB; n=12) or severe (SNEB; n=12) NEB groups. MNEB cows were fed ad lib grass silage and 8 kg day-1 concentrates and milked once daily; SNEB cows were fed 25 kg day-1 silage and 4kg day-1 concentrate and milked three times daily. Measurements of body condition score and EB were used to select cows which showed extremes in EB from each group (MNEB, n=5; SNEB, n=5). Cows were slaughtered on days 6-7 of the first follicular wave after calving (mean number of days post-partum: MNEB mean 13.6 M-BM-1 0.75, range 11M-bM-^@M-^S15; SNEB mean 14.3 M-BM-1 0.56, range 13M-bM-^@M-^S16), based on daily transrectal ultrasonography.At slaughter the entire spleen was removed and weighed, and samples weighing 1 g were dissected, rinsed in RNase-free phosphate buffer, snap frozen in liquid nitrogen, stored for 4 h in dry ice, and subsequently stored at 80M-BM-0C.
2014-04-08 | E-GEOD-56589 | biostudies-arrayexpress
Project description:In high yielding dairy cows the liver undergoes extensive physiological and biochemical changes during the early postpartum period in an effort to re-establish metabolic homeostasis and to counteract the adverse effects of negative energy balance (NEB). These adaptations are likely to be mediated by significant alterations in hepatic gene expression. To gain new insights into these events an EB model was created using differential feeding and milking regimes to produce two groups of cows with either a mild (MNEB) (n=5) or severe NEB (SNEB) (n=6) status. Cows were slaughtered and liver tissues collected on days 6-7 of the first follicular wave postpartum. Using an AffymetrixM-BM-. 23k oligonucleotide bovine array to determine global gene expression in hepatic tissue of these cows, a total of 416 genes (189 up- and 227 down-regulated) were found to be altered by SNEB. Network analysis using Ingenuity Pathway Analysis revealed that SNEB was associated with widespread changes in gene expression classified into 36 gene networks including those associated with lipid metabolism, connective tissue development and function, cell signalling, cell cycle and metabolic diseases. Severe NEB cows displayed reduced expression of transcription activators and signal transducers that regulate the expression of genes and gene networks associated with cell signalling and tissue repair. These alterations are linked with increased expression of abnormal cell cycle and cellular proliferation associated pathways. This study provides new information and insights on the effect of SNEB on gene expression in high yielding Holstein Friesian dairy cows in the early postpartum period. Multiparous Holstein-Friesian cows (n=24) were blocked 2 weeks prior to expected calving date according to parity, body condition score, and previous lactation yield (average lactation 6477M-BM-1354kg) and randomly allocated to mild (MNEB; n=12) or severe (SNEB; n=12) NEB groups. MNEB cows were fed ad lib grass silage and 8 kg day-1 concentrates and milked once daily; SNEB cows were fed 25 kg day-1 silage and 4kg day-1 concentrate and milked three times daily. Measurements of body condition score and EB were used to select cows which showed extremes in EB from each group (MNEB, n=5; SNEB, n=6). Cows were slaughtered on days 6-7 of the first follicular wave after calving (mean number of days post-partum: MNEB mean 13.6 M-BM-1 0.75, range 11M-bM-^@M-^S15; SNEB mean 14.3 M-BM-1 0.56, range 13M-bM-^@M-^S16), based on daily transrectal ultrasonography.The entire liver was removed within 15 to 30 min after slaughter and weighed. Samples weighing approximately 1 g were dissected, rinsed in RNase free phosphate buffer, snap frozen in liquid nitrogen and stored at -80M-BM-:C.
2014-04-08 | E-GEOD-56547 | biostudies-arrayexpress
Project description:Negative energy balance (NEB) is an altered metabolic state in high yielding cows that occurs during the first few weeks postpartum when energy demands for lactation and maintenance exceed the energy supply from dietary intake. NEB can, in turn, lead to metabolic disorders and to reduced fertility. Alterations in the expression of more than 700 hepatic genes have previously been reported in a study of NEB in postpartum dairy cows. miRNAs (microRNA) are known to mediate many alterations in gene expression post transcriptionally. To study the hepatic miRNA content of postpartum dairy cows, including their overall abundance and differential expression, in mild NEB (MNEB) and severe NEB (SNEB) short read RNA sequencing was carried out.
2014-03-14 | GSE55882 | GEO
Project description:In high yielding dairy cows the liver undergoes extensive physiological and biochemical changes during the early postpartum period in an effort to re-establish metabolic homeostasis and to counteract the adverse effects of negative energy balance (NEB). These adaptations are likely to be mediated by significant alterations in hepatic gene expression. To gain new insights into these events an EB model was created using differential feeding and milking regimes to produce two groups of cows with either a mild (MNEB) (n=5) or severe NEB (SNEB) (n=6) status. Cows were slaughtered and liver tissues collected on days 6-7 of the first follicular wave postpartum. Using an Affymetrix® 23k oligonucleotide bovine array to determine global gene expression in hepatic tissue of these cows, a total of 416 genes (189 up- and 227 down-regulated) were found to be altered by SNEB. Network analysis using Ingenuity Pathway Analysis revealed that SNEB was associated with widespread changes in gene expression classified into 36 gene networks including those associated with lipid metabolism, connective tissue development and function, cell signalling, cell cycle and metabolic diseases. Severe NEB cows displayed reduced expression of transcription activators and signal transducers that regulate the expression of genes and gene networks associated with cell signalling and tissue repair. These alterations are linked with increased expression of abnormal cell cycle and cellular proliferation associated pathways. This study provides new information and insights on the effect of SNEB on gene expression in high yielding Holstein Friesian dairy cows in the early postpartum period.
2014-04-08 | GSE56547 | GEO
Project description:Increased energy demands to support lactation, coupled with lowered feed intake capacity results in negative energy balance (NEB) and is typically characterized by extensive mobilization of body energy reserves in the early postpartum dairy cow. The catabolism of stored lipid leads to an increase in the systemic concentrations of nonesterified fatty acids (NEFA) and -hydroxy butyrate (BHB). Oxidation of NEFA in the liver result in the increased production of reactive oxygen species and the onset of oxidative stress and can lead to disruption of normal metabolism and physiology. The immune system is depressed in the peripartum period and early lactation and dairy cows are therefore more vulnerable to bacterial infections causing mastitis and or endometritis at this time. A bovine Affymetrix oligonucleotide array was used to determine global gene expression in the spleen of dairy cows in the early postpartum period. Spleen tissue was removed post mortem from five severe NEB (SNEB) and five medium NEB (MNEB) cows 15 days postpartum.SNEB increased systemic concentrations of NEFA and BHB, and white blood cell and lymphocyte numbers were decreased in SNEB animals. A total of 545 genes were altered by SNEB. Network analysis using Ingenuity Pathway Analysis revealed that SNEB was associated with NRF2-mediated oxidative stress, mitochondrial dysfunction, endoplasmic reticulum stress, natural killer cell signaling, p53 signaling, downregulation of IL-15, BCL-2, and IFN- ; upregulation of BAX and CHOP and increased apoptosis with a potential negative impact on innate and adaptive immunity.
2014-04-08 | GSE56589 | GEO