ABSTRACT: A functional genomics predictive network model identifies regulators of inflammatory bowel disease: Mount Sinai Hospital (MSH) Population Specimen Collection and Profiling of Inflammatory Bowel Disease
Project description:This study focuses on inflammatory bowel disease gene expression profiling. Surgical specimens from 134 patients undergoing bowel resection for inflammatory bowel disease (IBD) and non IBD controls at Mount Sinai Medical Center were collected as the source of tissue. Control samples (CLs) were harvested from normal non inflamed bowel located more than 10 cm away from the tumor from patients undergoing bowel resection for sporadic colon cancer. Ulcerative colitis (UC) and Crohn’s (CD) patient samples were all isolated from areas containing moderate to severe inflammation. The diagnostic pathology report for each specimen was provided by the Mount Sinai Hospital Pathology Department. Patients with UC and patients with CD shared common medications including corticosteroids, infliximab, azathioprine, and mesalamine.
Project description:Transcriptomic data was generated on uninvolved SB tissue from formalin-fixed paraffin-embedded (FFPE) small bowel resection margins of subjects requiring surgery at Cedars-Sinai Medical Center for Crohn’s disease.
Project description:To find predictive biomarkers for the development from inflammatory bowel disease unclassified (IBDU) to Crohn's disease(CD) or ulcerative colitis (UC), we performed short non-coding RNA profiling on IBDU patient samples at the time of diagnostic endoscopy.
Project description:We used microarrays to identify mucosal gene signatures predictive of response to infliximab (IFX) in patients with inflammatory bowel disease (IBD) and to gain more insight into the pathogenesis of IBD. Keywords: drug response and treatment effect
Project description:28 Pretreated Ewing sarcoma tumor blood samples were collected from the Hospital for Sick Children (SickKids) and Mount Sinai Hospital in Toronto, Canada in accordance with each institution’s Research Ethical Board (REB) guidelines. Detailed clinical information (age at presentation, gender, tumor site, stage, etc.) were obtained from the corresponding institutional tumor banks.
Transcriptome (RNA-Seq) sequencing was performed using established protocols on Illumina instruments.
Project description:Human brain samples from healthy and advanced Alzheimer's diseased patients were subjected to RNA-seq analysis to monitor RNA level changes during AD progression. Human brain samples were obtained from the Mount Sinai Brain Bank; RNA was Trizol extracted, ribominus selected and submitted for high-throughput sequencing.
Project description:Human brain samples from control and advanced Alzheimer's Diseased subjects were subjected to HITS-CLIP to monitor nELAVL binding changes during AD progression Human brain samples were obtained from the Mount Sinai Brain Bank; samples were UV-irradiated and subjected to nELAVL HITS-CLIP (detailed desription in accompanying paper)
