Dataset Information

PROPEL-16S amplicon

ABSTRACT: Daily supplementation with Lactobacillus reuteri DSM 17938 to extremely preterm infants modulated the gut microbiota during the first month of life in a randomised placebo-controlled trial

PROVIDER: PRJEB36531 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	ERR3887870.fastq.gz	Fastqsanger.gz
	ERR3887880.fastq.gz	Fastqsanger.gz
	ERR3887890.fastq.gz	Fastqsanger.gz
	ERR3887900.fastq.gz	Fastqsanger.gz
	ERR3887910.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 567

Similar Datasets

Project description:Surgery to correct trichiasis is a key component of the WHO trachoma control strategy, however unfavourable outcomes such as eyelid contour abnormalities (ECA) following surgery are relatively common. This study aimed to understand the transcriptional changes associated with the early development of ECA and the impact of doxycycline, which has anti-inflammatory and anti-fibrotic properties, upon these transcription patterns. One thousand Ethiopians undergoing trichiasis surgery were enrolled in a randomised controlled trial following informed consent. Equal groups of individuals were orally administered with 100mg/day of doxycycline or placebo for 28 days. Conjunctival swabs were collected immediately prior to surgery and at one- and six-months post-surgery. 3’ mRNA sequencing was performed on paired baseline and one-month samples from 48 individuals; 24 from each treatment group. Within each treatment group, 12 individuals developed ECA. Treatment and outcome groups were matched by age, sex and baseline disease severity. qPCR validation was then performed for 46 genes of interest in 145 individuals who developed ECA at one month and 145 matched controls, using samples from baseline, one and six months. All treatment/outcome groups upregulated genes associated with wound healing pathways at one month relative to baseline, however no differences were detected between groups. The summed expression of a highly coexpressed cluster of pro-fibrotic genes was higher in patients that developed ECA in the placebo group relative to controls. qPCR validation revealed that all genes in this cluster and a number of other pro-inflammatory genes were strongly associated with ECA, however these associations were not modulated by trial arm. The development of post-operative ECA is associated with overexpression of pro-inflammatory and pro-fibrotic genes including growth factors, matrix metalloproteinases, collagens and extracellular matrix proteins. There was no evidence that doxycycline modulated the association between gene expression and ECA.

Project description:Background: We tested the hypothesis that short-term supplementation with a physiological dose of folate can alter global gene expression in the colon of subjects with colorectal adenoma using a randomised double blind placebo controlled trial design. Materials and Methods: Fourteen subjects with histologically confirmed colorectal adenoma, randomised to receive folic acid (400M-BM-5g/d, n=6) or placebo (n=8) for 10 weeks, had blood samples and colonic tissue biopsies collected before and after the intervention. Blood samples were used to determine serum and red cell folate, plasma homocysteine, and genetic polymorphisms in methylenetetrahydrofolate reductase (MTHFR C677T) and methionine synthase (MS A2756G). RNA extracted from normal-appearing colonic tissue samples was used to determine global gene expression in the colon using AffymetrixM-oM-^CM-^R Microarray GeneChips. Microarray results were confirmed by quantitative real time RT-PCR. Two methods were used to analyse the microarray data: (1) differences between pre- and post-intervention gene expression values in the folic acid and placebo groups separately using paired-sample t tests; (2) differences between the folic acid and placebo groups in the ratio of post-intervention to pre-intervention gene expression values using independent sample t-tests. Results: (1) Following intervention, sixty seven genes were up-regulated and 13 genes were down-regulated in the folic acid group, while 21 genes were up-regulated and none were down-regulated in the placebo group (P<0.05, adjusted for multiple testing). (2) Thirty six genes were up-regulated and 18 genes were down-regulated in the folic acid group when compared with placebo, but none of these were statistically significant after adjustment for multiple testing. These genes are involved in multiple pathways, including cell cycle, signal transduction, cell differentiation, transport, cell division, cell motility, protein transport and immune response. There were no genes involved in 1-carbon metabolism that were altered in expression, although several genes involved in neoplasia were up-regulated. Conclusions: These results indicate that while folic acid can modify gene expression, it is difficult to separate its effects from the natural variability in gene expression in the colon. Fourteen patients with colorectal adenoma were treated with either folate supplementation (6 subjects) or a placebo (8 subjects) for 10 weeks in a randomised double-blind trial. Colonic biopsies of normal tissue were taken before and after the intervention, and analysed for gene expression.

Dataset Information

PROPEL-16S amplicon

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets