Project description:Genome-wide expression analysis of 182 extrahepatic cholangiocarcinoma and 38 non-tumoral bile duct samples as part of a integrated study of gene expression and targeted DNA-sequencing in patients with extrahepatic cholangiocarcinoma We used whole-genome transcriptome to conduct an unsupervised molecular classification of extrahepatic cholangiocarcinoma
Project description:Viral infection has a great impact on cellular expression profile of non-coding RNAs and genes. By microarray screening, our study identified 79 long non-coding RNAs (lncRNAs) and 140 mRNAs that were differentially expressed in human lung epithelial A549 cells infected with Zika virus (ZIKV). The bioinformatics analysis indicated that many differentially expressed lncRNAs were located in same chromosome as the differentially expressed mRNAs; and these lncRNAs and mRNAs were involved in the host responses to viral infection, including the innate immune response.
Project description:In order to understand the role of long noncoding RNAs (lncRNAs) and their interaction with coding RNAs in esophageal sqaumous cell cancer (ESCC), we performed genome-wide screening of the expression of lncRNAs and coding RNAs from primary ESCC tissue and adjacent normal tissue using Agilent SurePrint G3 Human GE 8x60K Microarray. By comparing ESCC tissues and matched normal tissues, differentially expressed lncRNAs and coding RNAs were identified and confirmed with PCR and other independent studies. We further identified a subset of co-located and co-expressed lncRNAs and coding RNAs using bioinformatic tools and the analysis suggested that a subset of lncRNAs may influence nearby genes involved in the genesis of ESCC. Four pairs of ESCC primary tumors and adjacent normal tissues were used for genome-scale microarray experiments, which included long noncoding RNAs and coding RNAs. Selected lncRNAs expressed in the experiment were validated on independent matched-pair samples with PCR method.
Project description:In order to understand the role of long noncoding RNAs (lncRNAs) and their interaction with coding RNAs in esophageal sqaumous cell cancer (ESCC), we performed genome-wide screening of the expression of lncRNAs and coding RNAs from primary ESCC tissue and adjacent normal tissue using Agilent SurePrint G3 Human GE 8x60K Microarray. By comparing ESCC tissues and matched normal tissues, differentially expressed lncRNAs and coding RNAs were identified and confirmed with PCR and other independent studies. We further identified a subset of co-located and co-expressed lncRNAs and coding RNAs using bioinformatic tools and the analysis suggested that a subset of lncRNAs may influence nearby genes involved in the genesis of ESCC.
Project description:<p>There is a clear need to develop biomarkers for Parkinson disease (PD) diagnosis and monitoring disease progression. In this study we evaluated cerebrospinal fluid (CSF) proteins, which are known to be critically involved in PD or identified in our preliminary profiling studies, aptamers, and RNAs as potential PD biomarkers. Access to subjects for this study was via the Pacific Northwest Udall Center (PANUC) and the Alzheimer's Disease Research Center (ADRC) at the University of Washington and Oregon Health and Sciences University (OHSU). Using CSF samples from 30 well-characterized patients with PD and 30 age-, sex-matched healthy controls, we prepared RNA seq libraries and performed deep sequencing of all RNA species, including small and long RNA, mRNAs, noncoding RNAs and differentially spliced transcripts. We then tried several methods for RNAseq data analysis to optimize our analysis pipeline. We identified a total of 3381 transcripts corresponding to 182 long intergenic RNAs (LincRNAs), 11 microRNAs (miRNAs), 2861 protein-coding transcripts, 200 pseudogenes and 127 antisense RNAs; some of them were differentially expressed between PD and control groups. Selected differentially expressed RNAs have been validated in the same set of CSF samples using real-time PCR (RT-PCR). Further validations in independent, larger cohorts of samples are still ongoing. Our results obtained so far suggested that CSF proteins and RNAs could be used as good indexes for PD diagnosis and disease severity/progression. This study is a part of the NIDDS-funded Parkinson's Disease Biomarkers Program (PDBP).</p>
Project description:The molecular mechanism of ECC in the genesis and progression is still unclear. Long non-coding RNAs (lncRNAs) have been shown to play critical regulatory roles in cancer biology. In order to understand lncRNAs expression patterns and their potential functional in ECC, we performed a transcriptome analysis of lncRNA and mRNA expression in ECC and paired adjacent noncancerous tissues using Agilent Human lncRNA +mRNA array V4.0 (4 × 180 K).
Project description:Oxaliplatin (L-OHP) serves as a standard chemotherapy for colorectal cancer, while the drug resistance is still a considerable challenge. A number of previously unknown transcripts have been identified in recent years, the vast majority of which are considered long non-coding RNA (lncRNA). Dysregulation of the lncRNA is involved in the genesis and progression of cancer. This RNA-seq was a paired-end sequencing and aimed to investigate the expression profile of lncRNA associated with oxaliplatin resistance in colorectal cancer.
Project description:Long noncoding RNAs (lncRNAs) have potential applications in clinical diagnosis and targeted cancer therapies. However, the expression profile of lncRNAs in colorectal cancer (CRC) initiation and progression is still unclear.In the present study, the expression profiles of lncRNAs and mRNAs were determined by microarray at specific tumor stages in an AOM/DSS-induced primary colon cancer model.
