Ontology highlight
ABSTRACT:
PROVIDER: PRJNA935267 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23462700.fastq.gz | Fastqsanger.gz | |||
| SRR23462701.fastq.gz | Fastqsanger.gz | |||
| SRR23462702.fastq.gz | Fastqsanger.gz | |||
| SRR23462703.fastq.gz | Fastqsanger.gz | |||
| SRR23462704.fastq.gz | Fastqsanger.gz |
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Project description:Proteases present in milk are heat-sensitive, and their activities increase or decrease depending on the intensity of the thermal treatment applied. The thermal effects on the protease activity are well-known for bovine milk but poorly understood for ovine and caprine milk. This study aimed to determine the nonspecific and specific protease activities in casein and whey fractions isolated from raw bovine, ovine and caprine milk collected in early lactation, and to determine the effects of low-temperature, long-time (63°C for 30 min) and high-temperature, short-time (85°C for 5 min) treatments on protease activities within each milk fraction.
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Project description:Mear prodution is the most important trait for sheep. In this study, we performed a Genome-wide association study (GWAS) by using Illumina Ovine SNP50 BeadChip in 329 purebred sheep phenotyped for 11 growth and meat production traits (birth weight, weaning weight, 6-month weight, eye muscle area, fat thickness, pre-weaning gain, post-weaning gain, daily weight gain, height at withers , chest girth and shin circumference). A total of 319 sheep and 48,198 SNPs were fitted using TASSEL 3.0 software as random effects in a mixed linear model. 36 chromosome-wise significant SNPs were identified for 7 traits and 10 of them reached genome-wide significance level consistently for post-weaning gain. Gene annotation was implemented based on the latest version3.1 ovine genome sequence (released October 2012), and meanwhile we referenced genomic information of human, bovine, mouse and rat. More than one-third SNPs (14 out of 36) were located within ovine genes , some other were located close to ovine genes (878bp-398165bp apart).
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Project description:Human intestinal epithelial organoids (IEO) culture models are rapidly emerging as novel experimental tools to investigate fundamental aspects of intestinal epithelial (patho)physiology. Cellular source and culture protocols vary between different IEO models and reliable markers for their characterization/validation are currently limited. Here, we provide the following reference datasets of transcriptomic profiling by RNA-sequencing: Purified intestinal epithelial cells (EpCAM+) from paediatric ileum and colon, Intestinal organoid cultures from paediatric ileum and colon, Purified intestinal epithelial cells (EpCAM+) from foetal small intestine and foetal large intestine, Intestinal organoid cultures from foetal small intestine and foetal large intestine, Intestinal organoid cultures derived from induced pluripotent stem cells.<br> Complementary data from methylation profiling on the same samples have been deposited at ArrayExpress under accession number E-MTAB-4957 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4957 ).</br>
2018-01-20 | E-MTAB-5015 | biostudies-arrayexpress
Project description:Ovine mastitis is defined as the inflammation of the sheep udder, most commonly caused in response to intramammary infections. Based on the occurrence of clinical signs, mastitis is characterized as either clinical or subclinical (SCM). The impact of ovine SCM on the overall sustainability of dairy sheep farms has been documented underpinning the significance of efficient diagnosis. Although SCM can be detected in cows, the performance and the validity of the methods used do not transfer in dairy sheep. This fact challenges the development of evidence-based ovine udder health management protocols and renders the detection and control of ovine mastitis rather problematic. Currently, cell culture-based models are being successfully used in biomedical studies and have also been effectively used in the case of bovine mastitis. The objective of the present study was to culture ovine primary mammary cells for the development of 2D and 3D cell culture-based models for the study of ovine SCM. Cells were infected by mastitis-inducing pathogens mimicking the pathogenesis of SCM as derived by natural intramammary infections. The secreted proteins were subjected to mass-spectrometry resulting in the identification of 79 distinct proteins. Among those, several had already been identified in healthy or mastitic milk, while others were detected for the first time in the ovine mammary secretome. The development of cell-based models for the early detection and the overall study of SCM has the potential to be applicable and beneficial for the udder health management in dairy sheep.
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Project description:In cattle, communication between endometrium and conceptus during the peri-implantation period is crucial for successful pregnancy. Understanding these interactions is vital as most early pregnancy loss occurs during this time. A major challenge in understanding uterine function and early pregnancy is lack of appropriate in-vitro models. Two-dimensional models are available, but do not recapitulate the endometrium’s complex multicellular structure. Here, we describe a hormonally responsive organoid model of the bovine endometrium, developed as a tool for studying endometrial function and early pregnancy. Bovine glandular epithelial cells were isolated from reproductive tracts and cultured in an extracellular matrix hydrogel (Cultrex 2) at 38.5°C, 5% CO (n=3). RNA was extracted and qPCR confirmed the presence of gland markers: leukemia inhibitory factor, mucin-1, insulin-like growth factor binding protein-1, kruppel-like factor-5 and forkhead box protein-A2. Organoids were imaged at specific time-points to monitor growth and passaged 3 times in 1:2 or 1:3 ratios after growing for a minimum of 10 days per passage. Morphologically, organoids were spherical and fast-growing at passages 0 and 1, but this declines following passage 2. Bovine endometrial organoids (n=3, passage 0) were treated with 1000 ng/ml recombinant ovine Interferon Tau (IFNT) or 10 μg/ml progesterone (P4) for 24 hours and analysed by RNASeq to assess hormone responsiveness. Differential expression analysis by DeSeq2 negative binomial distribution model followed by Wald test and Benjamini-Hochberg correction identified 373 transcripts significantly upregulated (padj<0.05 or log2fold change >0.05) in response to P4 treatment, with downstream analysis showing significant overrepresentation (FDR<0.05) of genes associated with positive regulation of protein localisation to plasma membrane and cell periphery. Of the 240 genes significantly downregulated by P4 these were significantly overrepresented (FDR<0.05) in biological processes of cilium and cytoskeleton organisation. IFNT treatment resulted in significant upregulation of 414 genes and downregulation of 119 genes. The largest cluster associated with differentially expressed genes in response to IFNT is defence to virus and interferon signalling. There were 30 genes altered by both P4 treatment and IFNT treatment. Organoids were also shown to express conserved microRNAs, and it was possible to culture them in a microfluidics device - making them a useful model for a multitude of potential investigations. This model provides a tool to investigate bovine endometrial function and peri-implantation communication, subsequently allowing species comparison to understand diversity in reproductive strategies.
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