Individualized microbiotas dictate impact of dietary fibre on colitis sensitivity
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PROVIDER: PRJEB64164 | ENA |
REPOSITORIES: ENA
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Project description:0dpa Fibre vs epidermal laser capture microdisection comparison Keywords: Development
2006-06-27 | GSE5133 | GEO
Project description:0dpa Fibre vs epidermal laser capture microdisection comparison Total RNA was isolated from each cell type (fibre initial or non-fibre epidermal pavement cell) from both Plant 1 and Plant 2. Hence, there were two biological replicates of each cell-type. Sub-samples of each cell type, designated here as technical replicates, were taken as separate batches of cells from different groups of ovules, but each from the same pair of plants. In particular, there were four sub-samples of fibre initial cells from plant 1 and two from plant 2 and two sub-samples of non-fibre epidermal from plant 1 and four from plant 2. The complete experiment involved three dye-swap pairs using a total of 6 arrays.
2006-06-26 | E-GEOD-5133 | biostudies-arrayexpress
Project description:Bacillus velezensis strain:VTX20 | isolate:dietary fibre Genome sequencing
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Project description:A gene expression profiling study on two major cotton species that are cultivated for fibre, Gossypium hirsutum (L.) and Gossypium barbadense (L.), at different stages during fibre development using a printed cDNA microarray was undertaken to identify potential candidate genes for manipulation to improve fibre quality. Keywords: Species comparison, development
2009-07-21 | GSE10363 | GEO
Project description:Background: Macrophages represent an important part of the immune system in the intestine and are crucial for maintaining homeostasis. As part of research investigating the effect of dietary fibres on the intestinal immune barrier THP-1 macrophages were used as model system. Methods: THP-1 monocytes were stimulated for 48 hours with 100 ng/ml PMA and 48 hours rested in medium. Subsequently, they were stimulated with 500 ug/ml dietary fibres and the maximal observed LPS contamination to serve as background control. After 6 hours, total RNA was extracted and Affymterix Human Gene 1.1 ST arrays were used to analyze the gene expression profiles. To identify dietary fibre induced gene expression profiles in dietary fibre gene responses were compared to medium samples. Furthermore, to analyse differentiatlly affected pathways Ingenuite Pathway Analysis was employed. Results: There was a clear difference in significantly differentially expressed genes (gene cut-off p<0.05) with beta-glucan oat medium viscosity and GOS changing transcription of a relative small amount of genes and Sugar beet pectin and Resistant starch a relative large amount of genes. These latter two were also the only dietary fibres to demonstrate an increase in Fc-receptor-related pathway activation. Alternatively, beta-glucan oat medium viscosity and GOS were the only dietary fibres to activate pathways related to cellular movement and the only two to not activate the Ahr-signaling pathway (p<0.05). Conclusion: our data indicate that the in vitro THP-1 macrophage model can be used to differentiate in immunomodulatory potential of dietary fibres and provide hypotheses for functional differentiation.
2022-05-30 | GSE99611 | GEO
Project description:The source of most errors in RNA sequencing (RNA-seq) read alignment is in the repetitive structure of the genome and not with the alignment algorithm. Genetic variation away from the reference sequence exacerbates this problem causing reads to be assigned to the wrong location. We developed a method, implemented as the software package Seqnature, to construct the imputed genomes of individuals (individualized genomes) of experimental model organisms including inbred mouse strains and genetically unique outbred animals. Alignment to individualized genomes increases read mapping accuracy and improves transcript abundance estimates. In an application to expression QTL mapping, this approach corrected erroneous linkages and unmasked thousands of hidden associations. Individualized genomes accounting for genetic variation will be useful for human short-read sequencing and other sequencing applications including ChIP-seq.
2014-06-10 | GSE45684 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE38560: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (RNA-seq) GSE38561: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (ChIP-seq) GSE38562: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (genomic SEQ) GSE38563: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (MNase-seq) GSE38564: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (5) Refer to individual Series
2012-06-11 | E-GEOD-38577 | biostudies-arrayexpress
Project description:A gene expression profiling study on two major cotton species that are cultivated for fibre, Gossypium hirsutum (L.) and Gossypium barbadense (L.), at different stages during fibre development using a printed cDNA microarray was undertaken to identify potential candidate genes for manipulation to improve fibre quality. Keywords: Species comparison, development Three-condition experiment: 7, 11 and 21 day post anthesis. Biological replicates: 3, Two species compared at each condition: Gossypium.hirsutum and Gossypium.barbadense. One replicate per array, dye swap, one rep per array.
2010-05-16 | E-GEOD-10363 | biostudies-arrayexpress
Project description:Background: Human intestinal tissue samples are barely accessible to study potential health benefits of nutritional compounds. Dietary fibres have been descirbed to be beneficial for intestinal health. Therefore, in this study we explored the applicability of an in vitro model, namely human intestinal Caco-2 cells, to study the effect of dietary fibres on intestinal health. Transcriptomics was applied to obtain more insight into their mode of actions in the intestinal cells. Methods: Caco-2 cells were stimulated with 500 ug/ml dietary fibres and the maximal observed LPS contamination to serve as background control for 6 hours, total RNA was extracted and Affymterix Human Gene 1.1 ST arrays were used to analyze the gene expression profiles. To identify dietary fibre induced gene expression profiles in dietary fibre gene responses were compared to medium samples. Furthermore, to analyse differentiatlly affected pathways Ingenuite Pathway Analysis was employed. Results: Pathway analysis revealed a distinct separation between the dietary fibres. GOS and beta-glucan oat medium viscosity affected transcription of a lower amount of genes (gene cut-off p<0.05) and gen transcription changes suggest an increase in vesicle transport and altered cholesterol regulation. On the other hand, the other dietary fibres differentially regulated a larger numbers of genes (gene cut-off p<0.05) and all appeared related to immune responses. We observed an increase in intracellular and extracellular anti-bacterial pathways and production of cytokines specifically aimed at communication with the adaptive immune system. Conclusion: GOS and beta-glucan oat medium viscosity appeared to induce intestinal epithelial communication with the body, whereas the other dietary fibres appeared recognized as PAMP and induce epithelial cells to interact with the immune system.
2022-05-30 | GSE99610 | GEO
Project description:The source of most errors in RNA sequencing (RNA-seq) read alignment is in the repetitive structure of the genome and not with the alignment algorithm. Genetic variation away from the reference sequence exacerbates this problem causing reads to be assigned to the wrong location. We developed a method, implemented as the software package Seqnature, to construct the imputed genomes of individuals (individualized genomes) of experimental model organisms including inbred mouse strains and genetically unique outbred animals. Alignment to individualized genomes increases read mapping accuracy and improves transcript abundance estimates. In an application to expression QTL mapping, this approach corrected erroneous linkages and unmasked thousands of hidden associations. Individualized genomes accounting for genetic variation will be useful for human short-read sequencing and other sequencing applications including ChIP-seq. Illumina 100bp single-end liver RNA-seq from 277 male and female Diversity Outbred 26-week old mice raised on standard chow or high fat diet. In addition, Illumina 100bp single-end liver RNA-seq from 128 male 26-week old male mice (20 weeks for NZO strain) from each of the DO founder strains raised on standard chow or high fat diet (8 males per strain by diet group). Each sample was sequenced in 2-4x technical replicates across multiple flowcells. Samples were randomly assigned lanes and multiplexed at 12-24x.
2014-06-10 | E-GEOD-45684 | biostudies-arrayexpress