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EPIC-Italy at HuGeF

ABSTRACT: This Series contains data from 845 participants (188 men and 657 women) in the EPIC-Italy cohort that was produced at the Human Genetics Foundation (HuGeF) in Turin, Italy. At the last follow-up (2010), 424 participants remained cancer-free, 235 had developed primary breast cancer, 166 had developed primary colorectal cancer, and 20 had developed other primary cancers. Anthropometric measurements, and dietary and lifestyle information obtained by questionnaire are also available.

ORGANISM(S): Homo sapiens

PROVIDER: GSE51032 | GEO | 2013/09/20

SECONDARY ACCESSION(S): PRJNA219744

REPOSITORIES: GEO

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EPIC-Italy at HuGeF

Project description:This Series contains data from 845 participants (188 men and 657 women) in the EPIC-Italy cohort that was produced at the Human Genetics Foundation (HuGeF) in Turin, Italy. At the last follow-up (2010), 424 participants remained cancer-free, 235 had developed primary breast cancer, 166 had developed primary colorectal cancer, and 20 had developed other primary cancers. Anthropometric measurements, and dietary and lifestyle information obtained by questionnaire are also available. A total of 845 samples from the EPIC-Italy cohort were analyzed.

2013-09-20 | E-GEOD-51032 | biostudies-arrayexpress

European eel Anguilla anguilla individuals from high (Tiber river, Italy) and low pollution (Bolsena lake, Italy) environments

Project description:An European eel-specific microarray platform was developed to identify genes involved in response to pollutants A comparative analysis of gene expression was conducted between European eel Anguilla anguilla individuals from high (Tiber river, Italy) and low pollution (Bolsena lake, Italy) environments. Gene expression profiling was performed using an European eel-specific oligo-DNA microarray of 14,913 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

2013-05-22 | E-GEOD-35055 | biostudies-arrayexpress

Arabidopsis thaliana ecotypes Rodasen-47 (Sweden) and Castelnuovo-12 (Italy) grown in high light and/or cold

Project description:Illumina HiSeq RNAseq data from the youngest fully developed leaf collected from two ecotypes of Arabidopsis thaliana, Rodasen-47 (Sweden) and Castelnuovo-12 (Italy), adapted to contrasting local climates, grown at different temperatures and/or light levels. Plants were all vegatively growing in one gallon pots to prevent root bounding. Plants were sampled at the 40th day of growth.

2020-07-14 | GSE154349 | GEO

Human Dental Calculus_Neolithic_Southern Italy

Project description:Characterisation of the metaproteome of a dental calculus sample extracted from a Neolithic burial, San Lorenzo Bellizzi, Italy (CS).

2023-10-24 | PXD039654 | Pride

Transcriptome of non-involved lung parenchyma from smoker lung adenocarcinoma patients from Milan, Italy.

Project description:Scientific evidence indicates that genetic factors may contribute to differences in lung cancer risk for individuals with similar levels of tobacco exposure, which is the main environmental risk factor of lung cancer. Moreover, lung cancer patients show large differences in clinical staging and survival; these differences seem to be attributable, at least partially, to the genetic background. The analysis of the molecular properties (e.g., germline variations and genome-wide expression levels) of non-involved tissue from lung cancer patients may contribute in the identification of genetic factors involved in the development and progression of this pathology. To this aim, we analyzed two series (discovery series, n = 204, and validation series, n = 78) of non-tumor lung tissue samples from smokers that underwent surgical lobectomy for adenocarcinoma in Milan, Italy. First, we examined the whole transcriptome of these two series to define the candidate genes and pathways associated with either lung cancer risk or prognosis in this cohort. Moreover, as sex and age are known to strongly influence the pathophysiology of human lungs, we used transcriptome data from the same samples to identify sex- and age-related transcriptional differences in lung. Samples of non-involved (apparently normal) lung parenchyma excised from patients who underwent lobectomy for lung adenocarcinoma in the area around Milan, Italy. The samples were analyzed in two sets: a discovery series (n = 204) and a validation series (n = 78).

2016-01-20 | E-GEOD-71181 | biostudies-arrayexpress

Identification of early response genes to Pratylenchus coffeae in resistant ramie by digital gene expression analysis (leaves)

Project description:Comparative transcriptome analysis was performed to study differentially expressed genes (DEGs) between CK and Cocytodes caerulea Guenée challenged (CH) leaves of ramie.We obtained 40.2 and 62.8 million reads for CH and CK libraries respectively.De novo assembling of these reads generated 26,759 and 29,988 unigenes respectively. After a integrate assembly for all data of these two libraries, a total of 46,533 unigenes with an average length of 845 bp were obtained.A total of 1179 genes were identified as DEGs, 657 and 1230 of them were up- and down- regulated respectively, in response to C.caerulea infestation. Leaf samples of Cocytodes caerulea infested (T2) and un-infested (T1) ramie were RNA-Seq sequenced to compare differented expressed genes.

2015-03-04 | E-GEOD-66447 | biostudies-arrayexpress

The Microbiome, Epigenome, and Diet in Adults with Obesity During Behavioral Weight Loss

Project description:Whole blood, stool samples, and questionnaire data were collected from participants in the DRIFT2 trial at baseline and at a 3 month follow-up visit to analyze relationships between DNA methylation, gut microbes, and diet data. 128 total whole blood samples were collected .

2023-08-30 | GSE240184 | GEO

Genome-wide expression analysis of ramie [Boehmeria nivea (L.) Gaudich] genes in response to ramie moth [Cocytodes coerulea Guenée] infestation

Project description:Comparative transcriptome analysis was performed to study differentially expressed genes (DEGs) between Cocytodes caerulea Guenée challenged (CH) and unchallenged (CK) leaves of ramie.We obtained 40.2 and 62.8 million reads for CH and CK libraries respectively.De novo assembling of these reads generated 26,759 and 29,988 unigenes respectively. After a integrate assembly for all data of these two libraries, a total of 46,533 unigenes with an average length of 845 bp were obtained.A total of 1179 genes were identified as DEGs, 657 and 1230 of them were up- and down- regulated respectively, in response to C.caerulea infestation.

2015-03-04 | GSE66447 | GEO

Subcutaneous adipose tissue: comparison of weight maintainence and weight regain following an 8-week low calorie diet

Project description:The present study was designed to identify determinants that foreshadow successful weight maintenance. More specifically, we examined whether subcutaneous adipose tissue (scAT) gene expression of participants who experience successful weight maintenance following caloric restriction differed from that of participants who regain weight. Forty women followed a dietary protocol consisting of an 8-week low calorie diet (LCD) and a 6-month weight maintenance phase. At the end of the protocol, participants were classified as weight maintainers (WM; 0-10% weight regain) and weight regainers (WR; 50-100% weight regain). Anthropometric measurements, plasma parameters, and scAT biopsies were taken before and after the LCD. Adipose tissue gene expression profiles were studied in all individuals before and after the LCD.

2011-09-29 | E-GEOD-24432 | biostudies-arrayexpress

Transcriptome of non-involved lung parenchyma from smoker lung adenocarcinoma patients from Milan, Italy.

2016-01-20 | GSE71181 | GEO

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