Project description:Aim: To compare the overall transcriptional profile in healthy controls and celiac disease patients. This dataset, was used to evaluate if our in vitro model (intestinal intraepithelial lymphocytes, desccribed in doi:10.1016/j.jaut.2020.10242 ) is representative of the transcriptional profile in the intestine under healthy or inflammatory conditions. Samples: Upper colonoscopy biopsies from 5 control and 11 celiac disease patients were taken, total RNA was extracted and RNA-sequencing was performed (without replicates)
Project description:In this study, we grew primary breast epithelial cells from breast biopsies of healthy donors, five each of African Ancestry, European ancestry and those who identify as Hispanic using epithelial cell reprogramming assay growth method. Cells grown were sorted into luminal progenitors (CD49F+/EpCAM+, labelled as PP cells) and mature luminal (CD49F-/EpCAM+, labelled as NP cells) by flow cytometry. Flow sorted cells were subjected to RNA-seq.
Project description:Comprehensive analysis of molecular pathology requires a collection of reference samples representing normal tissues from healthy donors. There is a shortage now of the gene expression data for human healthy tissues. The available data can either lack biological replicates or represent tissues adjacent to tumors removed during surgery that have signs of pathology and inflammation. For the available limited collections of normal tissues from post mortal donors, there is a problem of data incompatibility, as different datasets were generated using different experimental platforms and cannot be merged in a single panel. Here, for the first time, we construct and deposited a gene expression database of normal human tissues based on uniformly screened original sequencing (Illumina HiSeq 3000) data. A total of 148 solid tissue samples representing 20 organs were taken from post-mortal human healthy donors killed in road accidents no later than 36 hours after death. Blood and bone marrow samples were taken from 6 and 11 healthy volunteers respectively. The materials were collected since 2012 and stored until gene expression profiles were obtained by using the same reagents and protocols. Data consistency was confirmed by hierarchical clustering and principal component analysis (PCA). Our data can be useful to all those working with the analysis of human gene expression.
Project description:Genome-wide transcriptional profiling of colonic biopsies endoscopically acquired from the rectosigmoid area of healthy donors and UC patients.
Project description:Transcriptional profiling of colon epithelial biopsies from ulcerative colitis patients and healthy control donors. Study aims to survey and analyze variation from disease in different GI regions. Keywords: disease state analysis
Project description:Transcriptional profiling of colon epithelial biopsies from ulcerative colitis patients and healthy control donors. Study aims to survey and analyze variation from disease in different GI regions. Keywords: disease state analysis Biopsies from a variety of anatomic locations, from patients of various treatment status or healthy controls.
Project description:In addition to the accumulation of pro-oncogenic mutations in the epithelial cells, the tumorigenic process involves the dysregulation of the interactions between the epithelial cells and their microenvironment, as well as alterations within the microenvironment itself. Therefore, investigating the causes of the loss of the normal tissue homeostasis in the earliest stages of breast cancer carcinogenesis is the necessary underpinning of an effective breast cancer prevention strategy. In order to comprehensively capture the transcriptomic alterations occurring in the breast in a precancerous stage, we examined a unique resource present in our institute including breast tissue biopsies donated by women two to six years prior to the clinical manifestation of breast cancer (labeled “susceptible normal tissue”) as well as specimens from healthy women. Donors in the two cohorts were at a premenopausal status and were matched according to age, racial background and menstrual phase. Both the susceptible and healthy breast tissues appear histologically normal. Upon microdissection of the three breast tissue compartments including epithelial, stromal and adipose tissue, transcriptomic analysis was performed. Upregulation of genes involved in lipid metabolism and fatty acid transport was observed also in the susceptible stroma and adipose tissue compartments, respectively.
