ExpressArt LBR RNAready for Solid tissues & Bacteria
Identification of Specific Long Non-Coding Ribonucleic Acid Signatures and Regulatory Networks in Prostate Cancer in Fine-Needle Aspiration Biopsies.
Prostate cancer (PCa) is one of the most common tumor in men and can be deadly, especially if left untreated. Most patients diagnosed PCa not only by fine needle aspiration (FNA) biopsy, but their treatment options are also largely driven by pathological findings obtained with this FNA specimens. It is widely believed that lncRNAs have a strong biological significance, but their specific functions and regulatory networks have not been described. LncRNAs can serve as a key player and a regulator of carcinogenesis PCa and could become a new biomarker of this cancer.
To identify potential markers for early detection of PCa, in this study, we employed RNA endogenous compete (Cerna) microarray to identify lncRNAs differentially expressed (DelncRNAs) in PCa tissue and quantitative real-time PCR (qRT-PCR) analysis to validate this DelncRNAs in FNA biopsy. We show that a total of 451 lncRNAs were differentially expressed in the four pairs of PCa / adjacent tissue, and upregulation of lncRNAs RP11-33A14.1, RP11-423H2.3, and LAMTOR5-AS1 confirmed in FNA biopsy of PCa by qRT-PCR and consistent with the data array Cerna. The relationship between the expression of lncRNA LAMTOR5-AS1 and aggressive cancer was also investigated.
DelncRNAs regulation of network analysis shows that targeted RP11-423H2.3 RP11-33A14.1 lncRNAs and miR-7, miR-24-3p and miR-30 and interact with the RNA binding protein FUS. Knockdown of this DelncRNAs in PCa cells also showed RP11-423H2.3 effects of miR-7 / miR-24 / miR-30 or LAMTOR5-AS1 miR-942-5p / miR-542-3p through direct interaction. The results showed that three specific signature of this lncRNA and regulatory networks could serve as predictive of risk and diagnostic biomarkers for prostate cancer, even in biopsies obtained by FNA.
Identification of Specific Long Non-Coding Ribonucleic Acid Signatures and Regulatory Networks in Prostate Cancer in Fine-Needle Aspiration Biopsies.
Read Transcript Mapping and Assembly: A Scalable and High-throughput workflow for Processing and Analysis of Ribonucleic Acid Sequencing data.
RNA-generation sequencing is a very powerful way of generating a snapshot of the state transcriptomic in cells, tissues, or whole organisms. As the questions addressed by RNA-sequencing (RNA-seq) become both more complex and greater in number, there is a need to simplify the processing of RNA-Seq workflow, making them more efficient and interoperable, and able to handle both small and large datasets. It is very important for researchers who need to process hundreds to tens of thousands of RNA-Seq datasets.
To address this need, we have developed a scalable, user-friendly, and easily deployable analysis suite called RMTA (Read Mapping, Transcript Assembly). RMTA can easily process thousands of RNA-Seq datasets with features that include automatic analysis of the quality of reading, filter for low expressed transcripts, and read calculation for differential expression analysis.
RMTA is boxed using Docker for easy deployment in any computing environment [cloud, local, or high-performance computing (HPC)] and is available as two applications in CyVerse Discovery Environment, one for normal use and one specifically designed to introduce students and high school for analysis of RNA-seq.
For very large datasets (tens of thousands of files FASTq) we developed a high-throughput, scalable and parallelized version of RMTA optimized for launching the Open Science Grid (OSG) of the Environmental Discovery. OSG-RMTA allows users to utilize the Environmental Discovery for data management, parallelization, and send the job to OSG, and finally, employing OSG to be distributed, high-throughput computing.
Description: Human cerebral cortex tissue lysate was prepared by homogenization using a proprietary technique. The tissue was frozen in liquid nitrogen immediately after excision and then stored at -70°C. The human cerebral cortex tissue total protein is provided in a buffer including HEPES (pH7.9), MgCl2, KCl, EDTA, Sucrose, Glycerol, Sodium deoxycholate, NP-40, and a cocktail of protease inhibitors. For quality control purposes, the cerebral cortex tissue pattern on SDS-PAGE gel is shown to be consistent for each lot by visualization with coomassie blue staining. The cerebral cortex tissue is then Western analyzed by either GAPDH or β-actin antibody, and the expression level is consistent with each lot.
Description: Human brain cerebral Cortex tissue membrane protein lysate was prepared by isolating the membrane protein from whole tissue homogenates using a proprietary technique. The human cerebral Cortex tissue was frozen in liquid nitrogen immediately after excision and then stored at -70°C. The membrane protein is provided in a buffer including HEPES (pH 7.9), MgCl2, KCl, EDTA, Sucrose, Glycerol, sodium deoxycholate, NP-40, and a cocktail of protease inhibitors. For quality control purposes, the isolated brain cerebral Cortex tissue membrane protein pattern on SDS-PAGE gel is shown to be consistent for each lot by visualization with coomassie blue staining. The isolated brain cerebral Cortex tissue membrane protein is then Western analyzed by either GAPDH or β-actin antibody to confirm there is no signal or very weak signal.
Description: Mouse Neural Stem Cells (MNSC) are multipotent, and can be induced to differentiate into neurons, astrocytes and oligodendrocytes that make up the central nervous system (CNS). Neurospheres transplanted into intact brain can survive, expand and differentiate into mature neurons, astrocytes and oligodendrocytes in 3 weeks. The ability of neural stem cells to retain multi-lineage potential and proliferate extensively in vitro provides new avenues for the treatment of neural degenerative diseases and injuries.Isolated from fetal or adult mouse brains, MNSC are maintained in an undifferentiated, proliferative state by culturing them as free floating neurospheres in serum-free medium optimized with growth factors. MNSC are cryopreserved at first passage and can be cultured and propagated for 1-2 passages prior to induction of phenotypic differentiation. Differentiated MNSCs are positive for β-tubulin III, GFAP and the oligodendrocyte marker O4 when cultured in Mouse Neural Differentiation Medium. The cells form neurospheres in Mat Neural Stem Cell Growth Medium.
*Innovative Grade US Origin Mouse Cerebral Cortex Tissue Lysate
Or, OSG-RMTA can be run directly on the OSG via the command line. RMTA designed to be useful for scientists of data, of any skill level, interest quickly and reproducibly analyze large data sets of RNA-seq them.
