Ontology highlight
ABSTRACT:
PROVIDER: PRJNA507259 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8249134_1.fastq.gz | Fastqsanger.gz | |||
| SRR8249134_2.fastq.gz | Fastqsanger.gz | |||
| SRR8249135_1.fastq.gz | Fastqsanger.gz | |||
| SRR8249135_2.fastq.gz | Fastqsanger.gz | |||
| SRR8249136_1.fastq.gz | Fastqsanger.gz |
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Project description:Transciprional profiling of horn forming region of Bos taurus comparing horned, polled and scurred cattle.
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Project description:Transciprional profiling of horn forming region of Bos taurus comparing horned, polled and scurred cattle. 3 condition experiment, Polled vs Horned, Polled vs Scurred, Scurred vs Horned, male and female samples, including dye swaps. 5 chips. No confounding between sex and chip. No confounding between indivdual and chip.
2010-05-01 | E-GEOD-21585 | biostudies-arrayexpress
Project description:Heat stress has a detrimental impact on cattle health, welfare and productivity by affecting gene expression, metabolism and immune response, but little is known on the epigenetic mechanisms mediating the effect of temperatureat the cellular and organism level. In this study, we investigated genome-wide DNA methylation in blood samples collected from 5 bulls of the heat stress resilient Nellore breed and 5 bulls of the Angus that are more heat stress susceptible, exposed to the sun and high temperature-high humidity during the summer season of the Brazilian South-East region. The methylomes were analyzed during and after the exposure by Reduced Representation Bisulfite Sequencing, which provided genome-wide single-base resolution methylation profiles. Significant methylation changes between stressful and recovery periods were observed in 822 genes. Among these, 352 were only seen in Angus, 367 were specific to Nellore, and 103 showed significant changes in methylation patterns in both breeds. KEGG and Gene Ontology (GO) enrichment analyses showed that responses were breed-specific. Interestingly, in Nellore significant genes and pathways were mainly involved in stress responses and cellular defense and were undermethylated during heat stress. Whereas in Angus the response was less focused. These preliminary results suggest that heat challenge induces changes in methylation patterns in specific loci, which should be further scrutinized to assess their role in heat tolerance.
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Project description:Transcription profiling of horned and polled and scurs cattle
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Project description:The purpose of this research was to investigate the causes and consequences of pHu variations in beef cattle. For that, were evaluated 176 Nellore beef cattle, and classified into two different pHu groups: High (≥6.0, N=17) and Normal (<5.8, N=159). Plasma concentrations of cortisol and adrenocorticotropic hormone, lactate and glycogen muscular content, meat color, shear force and Longissimus thoracis muscle proteomic profile were evaluated and compared between pHu groups. Muscle glycogen content, meat color and shear force statistically differed between pHu groups. Label-free quantitative proteomic analysis revealed ten differentially abundant proteins between pHu groups, involved in metabolic processes and muscle contraction. Thirty-six and 31 proteins were exclusively present in Normal and High pHu group, respectively, which were related to TCA cycle, cortisol production, calcium regulation, and antioxidant function. The MYH7, UGP2, and VDAC3 were identified as potential indicators of pHu variations. CALM and NNT appeared to be interesting proteins to better understand the metabolic pathways behind pHu.
2018-07-11 | PXD009320 | Pride
Project description:Background: The Malnad Gidda are unique dwarf Bos indicus cattle native to heavy rainfall Malnad and coastal areas of Karnataka in India. These cattle are highly adapted to harsh climatic conditions and are more resistant to Foot and Mouth disease as compared to other breeds of B.indicus. Since the first genome reference became available from B.taurus Hereford breed, only a few other breeds have been genotyped using high-throughput platforms. Also despite the known reports on high diversity within indicine breeds as compared to taurine breeds, only one draft genome of Nellore and horn transcriptome of Kankrej breed were sequenced at base level resolution. Because of the special characteristics Malnad Gidda possess, it becomes the choice of breed among many indicine cows to study at molecular level and genotyping. Results: Sequencing mRNA from the PBMCs isolated from blood of one selected Malnad Gidda bull resulted in generation of 55 million paired-end reads of 100bp length. Raw sequencing data is processed to trim the adaptor and low quality bases, and are aligned against the whole genome and transcript assemblies of Bos taurus UMD 3.1 and Bos indicus (Nellore breed) respectively. About 72% of the sequenced reads from our study could be mapped against the B.taurus genome where as only 41% of reads could be mapped against the Bos indicus transcript assembly. Transcript assembly from the alignment carried out against the annotated B.taurus UMD 3.1 genome resulted in identification of ~10,000 genes with significant expression (FPKM>1). In a similar analysis against the B.indicus Kankrej assembled transcripts we could identify only ~6,000 transcripts. From the variant analysis of the sequencing data we found ~10,000 SNPs in coding regions among which ~9,000 are novel and ~6,400 are amino acid changing. Conclusions: For the first time we have genotyped and explored the transcriptome of B.indicus Malnad Gidda breed. A comparative analysis of mapping the RNA-Seq data against the available reference genome and transcript sequences is demonstrated. An enhanced utility of transcript sequencing could be achieved by improving or completing the sequence assembly of any B.indicus breed to better characterize the indicine breeds for productivity features and selective breeding.
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Project description:Comparative muscle transcriptome associated with carcass traits of Nellore cattle
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