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Fresh fecal samples from patients with ulcerative colitis

ABSTRACT: fresh fecal samples from patients with ulcerative colitis Raw sequence reads

PROVIDER: PRJNA695366 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13608472.fastq.gz	Fastqsanger.gz
	SRR13608473.fastq.gz	Fastqsanger.gz
	SRR13608474.fastq.gz	Fastqsanger.gz
	SRR13608475.fastq.gz	Fastqsanger.gz
	SRR13608476.fastq.gz	Fastqsanger.gz

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Project description:Objective Crohn’s Disease (CD) and Ulcerative Colitis (UC) are chronic inflammatory diseases of the gastrointestinal tract. Reliable diagnosis of these diseases requires a comprehensive examination of the patient, which include invasive endoscopy. This study assesses whether non-invasive LC-MS/MS based analysis of microbial and human proteins from feces may support the diagnosis of the diseases. Design In order to mimic a representative clinical background for this study, we investigated 17 healthy controls, 11 CD patients, 14 UC patients, also 13 Irritable Bowel Disease (IBS) patients, 8 Colon Adenoma (CA) patients, and 8 Gastric Carcinoma (GCA) patients. The proteins were extracted from the fecal samples with liquid phenol in a ball mill. Subsequently, the proteins were digested tryptically to peptides and analyzed by liquid chromatography coupled to an Orbitrap MS/MS. For protein identification and interpretation of taxonomic and functional results, the MetaProteomeAnalyzer software and the UniProtKB/SwissProt database and several metagenomes from human fecal samples were used. Results Cluster analysis and ANOSIM show a separation of healthy controls from patients with CD and UC as well as from patients with GCA. Among others, UC and CD correlated with an increase of neutrophil extracellular traps and immunoglobulins G (IgG) as well as a decrease of IgA. A specific marker metaprotein for CD was an increase of the human enzyme sucrose-isomaltase. IBS and CA patient’s fecal metaproteome showed only minor alterations. Conclusion Metaproteome analysis distinguished between patients with UC, CD and healthy controls and is therefore useful as a non-invasive tool for routine diagnostics in hospitals.

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Methylation profiling in Ulcerative colitis

Project description:The series was designed to identify the different methylated single CpGs involved in the pathophysiology of ulcerative colitis. A cohort of n=20 monozygotic twins, discordant for ulcerative colitis was selected. Illumina and Nimblegen platforms were used.

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