Ontology highlight
ABSTRACT:
PROVIDER: PRJNA506987 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8247300_1.fastq.gz | Fastqsanger.gz | |||
| SRR8247300_2.fastq.gz | Fastqsanger.gz | |||
| SRR8247310_1.fastq.gz | Fastqsanger.gz | |||
| SRR8247310_2.fastq.gz | Fastqsanger.gz | |||
| SRR8247320_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 176 |
Similar Datasets
Project description:Yersinia enterocolitica, an important cause of human gastroenteritis generally caused by the consumption of livestock, has traditionally been categorized into three groups with respect to pathogenicity, i.e., nonpathogenic (biotype 1A), low pathogenicity (biotypes 2 to 5), and highly pathogenic (biotype 1B). However, genetic differences that explain variation in pathogenesis and whether different biotypes are associated with specific nonhuman hosts are largely unknown. In this study, we applied comparative phylogenomics (whole-genome comparisons of microbes with DNA microarrays combined with Bayesian phylogenies)to investigate a diverse collection of 94 strains of Y.enterocolitica consisting of 35 human, 35 pig, 15 sheep, and 9 cattle isolates from nonpathogenic, low-pathogenicity, and highly pathogenic biotypes. Analysis confirmed three distinct statistically supported clusters composed of a nonpathogenic clade, a low-pathogenicity clade, and a highly pathogenic clade. Genetic differences revealed 125 predicted coding sequences (CDSs) present in all highly pathogenic strains but absent from the other clades. These included several previously uncharacterized CDSs that may encode novel virulence determinants including a hemolysin, a metalloprotease, and a type III secretion effector protein. Additionally, 27 CDSs were identified which were present in all 47 low-pathogenicity strains and Y.enterocolitica 8081 but absent from all nonpathogenic 1A isolates. Analysis of the core gene set for Y.enterocolitica revealed that 20.8% of the genes were shared by all of the strains, confirming this species as highly heterogeneous, adding to the case for the existence of three subspecies of Y.enterocolitica. Further analysis revealed that Y.enterocolitica does not cluster according to source (host). Data is also available from http://bugs.sgul.ac.uk/E-BUGS-36
2006-06-20 | E-BUGS-36 | biostudies-arrayexpress
Project description:Genome-wide analysis of DNA methylation profiles from patients with Sjögren's syndrome with high versus low fatigue levels using the Illumina Infinium HumanMethylation450 Beadchip array. Background Chronic fatigue is a common, disabling, and poorly understood phenomenon. Recent studies indicate that epigenetic mechanisms may be involved in the expression of fatigue, a prominent feature of primary Sjögrenâs syndrome (pSS). The aim of this study was to investigate whether DNA methylation profiles of whole blood are associated with fatigue in patients with pSS. Methods 48 pSS patients with high (n=24) or low (n=24) fatigue as measured by a visual analogue scale were included. Genome-wide DNA methylation was investigated using the Illumina HumanMethylation450 BeadChip array. Case-case study including Sjögren's patients with high fatigue (n=24) and patients with low fatigue levels (n=24)
2015-12-04 | E-GEOD-75679 | biostudies-arrayexpress
Project description:miRNA expression profiles of PBMCs in healthy subjects following extra virgin olive oil intake. The aim of the present study was to investigate the whole-genome gene and miRNA profiles of PBMCs after EVOO intake. Results provide the information of changes in PBMPs transcriptome following EVOO intake.
2016-07-19 | GSE75026 | GEO
Project description:Gene expression profiles of PBMCs in healthy subjects following extra virgin olive oil intake. The aim of the present study was to investigate the whole-genome gene and miRNA profiles of after EVOO intake. Results provide the information of changes in PBMPs transcriptome following EVOO intake.
2016-07-19 | GSE75025 | GEO
Project description:Gene expression profiles of PBMCs in patients with MS following extra virgin olive oil intake. The aim of the present study was to investigate the whole-genome gene and miRNA profiles of after EVOO intake. Results provide the information of changes in PBMCs transcriptome following EVOO intake.
2016-07-19 | GSE84591 | GEO
Project description:Gene expression profiles of PBMCs in patients with MS following extra virgin olive oil intake. The aim of the present study was to investigate the whole-genome gene and miRNA profiles of after EVOO intake. Results provide the information of changes in PBMCs transcriptome following EVOO intake. RNA obtained from PBMCs of the same patients before and after extra virgin olive oil intake (paired samples). Comparisons: T0 vs. T1 (paired samples)
2016-07-19 | E-GEOD-84591 | biostudies-arrayexpress
Project description:Gene expression profiles of PBMCs in healthy subjects following extra virgin olive oil intake. The aim of the present study was to investigate the whole-genome gene and miRNA profiles of after EVOO intake. Results provide the information of changes in PBMPs transcriptome following EVOO intake. RNA obtained from PBMCs of the same subjects before and after extra virgin olive oil intake (paired samples). Comparisons: T0 vs. T1 (paired samples) - Controls
2016-07-19 | E-GEOD-75025 | biostudies-arrayexpress
Project description:Background: Despite of extensive research the genetic component of extremely low birth weight in newborns has remained obscure. Results: The aim of the case study was to identify candidate gene(s) causing extremely low birth weight (ELBW) in newborns and hypotrophy in infants. A four-member family was studied: mother, father and two ELBW-phenotype children. The studies were carried out due to the medical conditions of the second child at birth and post-partum: peculiar phenotype, micro-anomalies, recurrent infections, suspicion of autoimmune hepatitis, multifactorial encephalopathy, and suspicion of metabolic and chromosomal abnormalities. Whole genome single nucleotide polymorphism (SNP) genotyping array was used to investigate genomic rearrangements in both affected children using peripheral blood DNA samples. Whole blood transcriptome was assessed by using RNA sequencing (RNA-seq) in all four family members. RNA-seq identified a single gene – C14orf132 differentially expressed, with the level of the transcript significantly lower in blood samples of children. Copy number variant (CNV) analysis did not reveal any pathogenic CNVs in the region of C14orf132 gene of both affected children. Conclusion: We showed the importance of combining whole genome CNV and transcriptome analysis in identification of the candidate gene(s) in case studies. We propose the C14orf132 (chromosome 14 open reading frame 132) gene expression to be associated with the ELBW-phenotype. C14orf132 gene is a novel long non-coding RNA (lincRNA) with unknown function, which might be associated with the developmental delay through the altered gene expression Background: Despite of extensive research the genetic component of extremely low birth weight in newborns has remained obscure. Results: The aim of the case study was to identify candidate gene(s) causing extremely low birth weight (ELBW) in newborns and hypotrophy in infants. A four-member family was studied: mother, father and two ELBW-phenotype children. The studies were carried out due to the medical conditions of the second child at birth and post-partum: peculiar phenotype, micro-anomalies, recurrent infections, suspicion of autoimmune hepatitis, multifactorial encephalopathy, and suspicion of metabolic and chromosomal abnormalities. Whole genome single nucleotide polymorphism (SNP) genotyping array was used to investigate genomic rearrangements in both affected children using peripheral blood DNA samples. Whole blood transcriptome was assessed by using RNA sequencing (RNA-seq) in all four family members. RNA-seq identified a single gene – C14orf132 differentially expressed, with the level of the transcript significantly lower in blood samples of children. Copy number variant (CNV) analysis did not reveal any pathogenic CNVs in the region of C14orf132 gene of both affected children. Conclusion: We showed the importance of combining whole genome CNV and transcriptome analysis in identification of the candidate gene(s) in case studies. We propose the C14orf132 (chromosome 14 open reading frame 132) gene expression to be associated with the ELBW-phenotype. C14orf132 gene is a novel long non-coding RNA (lincRNA) with unknown function, which might be associated with the developmental delay through the altered gene expression Background: Despite of extensive research the genetic component of extremely low birth weight in newborns has remained obscure. Results: The aim of the case study was to identify candidate gene(s) causing extremely low birth weight (ELBW) in newborns and hypotrophy in infants. A four-member family was studied: mother, father and two ELBW-phenotype children. The studies were carried out due to the medical conditions of the second child at birth and post-partum: peculiar phenotype, micro-anomalies, recurrent infections, suspicion of autoimmune hepatitis, multifactorial encephalopathy, and suspicion of metabolic and chromosomal abnormalities. Whole genome single nucleotide polymorphism (SNP) genotyping array was used to investigate genomic rearrangements in both affected children using peripheral blood DNA samples. Whole blood transcriptome was assessed by using RNA sequencing (RNA-seq) in all four family members. RNA-seq identified a single gene – C14orf132 differentially expressed, with the level of the transcript significantly lower in blood samples of children. Copy number variant (CNV) analysis did not reveal any pathogenic CNVs in the region of C14orf132 gene of both affected children. Conclusion: We showed the importance of combining whole genome CNV and transcriptome analysis in identification of the candidate gene(s) in case studies. We propose the C14orf132 (chromosome 14 open reading frame 132) gene expression to be associated with the ELBW-phenotype. C14orf132 gene is a novel long non-coding RNA (lincRNA) with unknown function, which might be associated with the developmental delay through the altered gene expression. Background: Despite of extensive research the genetic component of extremely low birth weight in newborns has remained obscure. Results: The aim of the case study was to identify candidate gene(s) causing extremely low birth weight (ELBW) in newborns and hypotrophy in infants. A four-member family was studied: mother, father and two ELBW-phenotype children. The studies were carried out due to the medical conditions of the second child at birth and post-partum: peculiar phenotype, micro-anomalies, recurrent infections, suspicion of autoimmune hepatitis, multifactorial encephalopathy, and suspicion of metabolic and chromosomal abnormalities. Whole genome single nucleotide polymorphism (SNP) genotyping array was used to investigate genomic rearrangements in both affected children using peripheral blood DNA samples. Whole blood transcriptome was assessed by using RNA sequencing (RNA-seq) in all four family members. RNA-seq identified a single gene – C14orf132 differentially expressed, with the level of the transcript significantly lower in blood samples of children. Copy number variant (CNV) analysis did not reveal any pathogenic CNVs in the region of C14orf132 gene of both affected children. Conclusion: We showed the importance of combining whole genome CNV and transcriptome analysis in identification of the candidate gene(s) in case studies. We propose the C14orf132 (chromosome 14 open reading frame 132) gene expression to be associated with the ELBW-phenotype. C14orf132 gene is a novel long non-coding RNA (lincRNA) with unknown function, which might be associated with the developmental delay through the altered gene expression.
2016-08-01 | GSE85013 | GEO
Project description:miRNA expression profiles of PBMCs in healthy subjects following extra virgin olive oil intake. The aim of the present study was to investigate the whole-genome gene and miRNA profiles of PBMCs after EVOO intake. Results provide the information of changes in PBMPs transcriptome following EVOO intake. RNA obtained from PBMCs of the same patients before and after extra virgin olive oil intake (paired samples). Comparisons: T0 vs. T1 (paired samples) - Controls
2016-07-19 | E-GEOD-75026 | biostudies-arrayexpress