Dataset Information

Fecal metaproteome profiles of celiac disease patients with poly-autoimmunity

ABSTRACT: Twenty-eight subjects were selected for the study from among celiac disease patients regularly followed at the Medical Clinic of the University of Sassari. Celiac disease (CD) was diagnosed according to international guidelines. Patients were divided into two groups of 14 subjects based on the presence or absence of additional autoimmune diseases. Only autoimmune diseases confirmed by a specialist's certification were considered for the study. Further inclusion criteria included a body mass index (BMI) between 18 and 25 kg/m², a gluten-free diet (GFD) duration of one year or more, and an age between 18 and 60 years. Exclusion criteria were: (i) use of antibiotics, probiotics, or prebiotics in the 3 months prior to enrollment; (ii) a vegetarian or vegan diet; (iii) a history of malignancy, pregnancy, alcohol abuse, or drug addiction. Following a clinical evaluation, each patient provided a fecal sample. Additionally, three questionnaires were collected concerning: i) anamnestic and anthropometric data, ii) gastrointestinal symptoms, and iii) dietary habits and lifestyle.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human) Human Gut Metagenome

TISSUE(S): Feces

DISEASE(S): Celiac Disease

SUBMITTER: Alessandro Tanca

LAB HEAD: Sergio Uzzau

PROVIDER: PXD069517 | Pride | 2025-10-16

REPOSITORIES: Pride

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			Action	DRS
	CD_28samples_3DBs.pdResult	Other
	CD_28samples_3DBs_intensity_norm_MasterProteins.xlsx	Xlsx
	CD_28samples_3DBs_intensity_norm_PSMs.xlsx	Xlsx
	CD_28samples_3DBs_intensity_norm_peptides.xlsx	Xlsx
	P-UMG-AT-luglio2019-11C.msf	Msf

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Project description:BACKGROUND: Microarray comparative genomic hybridization (CGH) is currently one of the most powerful techniques to measure DNA copy number in large genomes. In humans, microarray CGH is widely used to assess copy number variants in healthy individuals and copy number aberrations associated with various diseases, syndromes and disease susceptibility. In model organisms such as Caenorhabditis elegans (C. elegans) the technique has been applied to detect mutations, primarily deletions, in strains of interest. Although various constraints on oligonucleotide properties have been suggested to minimize non-specific hybridization and improve the data quality, there have been few experimental validations for CGH experiments. For genomic regions where strict design filters would limit the coverage it would also be useful to quantify the expected loss in data quality associated with relaxed design criteria. RESULTS: We have quantified the effects of filtering various oligonucleotide properties by measuring the resolving power for detecting deletions in the human and C. elegans genomes using NimbleGen microarrays. Approximately twice as many oligonucleotides are typically required to be affected by a deletion in human DNA samples in order to achieve the same statistical confidence as one would observe for a deletion in C. elegans. Surprisingly, the ability to detect deletions strongly depends on the oligonucleotide 15-mer count, which is defined as the sum of the genomic frequency of all the constituent 15-mers within the oligonucleotide. A similarity level above 80% to non-target sequences over the length of the probe produces significant cross-hybridization. We recommend the use of a fairly large melting temperature window of up to 10 C, the elimination of repeat sequences, the elimination of homopolymers longer than 5 nucleotides, and a threshold of -1 kcal/mol on the oligonucleotide self-folding energy. We observed very little difference in data quality when varying the oligonucleotide length between 50 and 70, and even when using an isothermal design strategy. CONCLUSIONS: We have determined experimentally the effects of varying several key oligonucleotide microarray design criteria for detection of deletions in C. elegans and humans with NimbleGen's CGH technology. Our oligonucleotide design recommendations should be applicable for CGH analysis in most species. One-copy deletions were studied in both the C. elegans (2 samples) and human (1 sample) genomes. There were no replicate or dye-swap hybridizations.

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Fecal metaproteome profiles of celiac disease patients with poly-autoimmunity

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