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Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in Human Trisomy 21 Hybridization- and tag-based technologies have been successfully used in Down syndrome to identify genes involved in various aspects of the pathogenesis. However, these technologies suffer from several limits and drawbacks and, to date, information about rare, even though relevant, RNA species such as long and small non-coding RNAs, is completely missing. Indeed, none of published works has still described the whole transcriptional landscape of Down syndrome. Although the recent advances in high-throughput RNA sequencing have revealed the complexity of transcriptomes, most of them rely on polyA enrichment protocols, able to detect only a small fraction of total RNA content. On the opposite end, massive-scale RNA sequencing on rRNA-depleted samples allows the survey of the complete set of coding and non-coding RNA species, now emerging as novel contributors to pathogenic mechanisms. Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in Human Trisomy 21
[BioC] a few questions on DESeq
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FTP Download Custom data sets If you want to filter or customise your download, please try Biomart , a web-based querying tool. API Code If you do not have access to CVS, you can obtain our latest API code as a gzipped tarball: Download complete API for this release FTP Download
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Galaxy | Published Page | Galaxy RNA-seq Analysis Exercise Galaxy | Published Page | Galaxy RNA-seq Analysis Exercise Galaxy provides the tools necessary to creating and executing a complete RNA-seq analysis pipeline. This exercise introduces these tools and guides you through a simple pipeline using some example datasets. Familiarity with Galaxy and the general concepts of RNA-seq analysis are useful for understanding this exercise. This exercise should take 1-2 hours. You can check your work by looking at the history and visualization at the bottom of this page, which contain the datasets for the completed exercise. Input Datasets
Galaxy
Whole Transcriptome Analysis
Seq Data Analysis Tools
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2010 Annual Report of the Division of Intramural Research, NICHD | Section on Eukaryotic DNA Replication and Gene Regulation
Figure 2 : Defining an epigenetic code : Nature Cell Biology In response to an environmental or intrinsic signal at the morula stage, a histone modification (red oval) occurs on nucleosomes packaging a regulatory region of gene A, in those cells destined to form the inner cell mass (ICM) of the blastocyst. Together with a pre-existing modification (blue oval) this generates a distinctive epigenetic 'sign'. There is no immediate change in transcription of gene A, but the sign is passed on to successive cell generations, in the absence of the initial signal. Figure 2 : Defining an epigenetic code : Nature Cell Biology
Taxonomy browser (Bos taurus) Genome Information See the NCBI Genome homepageGo to NCBI genomic BLAST page for Bos taurus External Information Resources (NCBI LinkOut) Notes: Groups interested in participating in the LinkOut program should visit the LinkOut home page. A list of our current non-bibliographic LinkOut providers can be found here. Taxonomy browser (Bos taurus)
The genome of the domestic cow, Bos taurus, was sequenced using a mixture of hierarchical and whole-genome shotgun sequencing methods. The sequences were assembled by the Center for Bioinformatics and Computational Biology at University of Maryland (CBCB) using the Celera Assembler [1]. Two major releases have been made available to the public: UMD2 (April 2009) [2] and UMD3.0 (August 2009) [3]. Bos taurus assembly Bos taurus assembly
RNA Seq - GQ Wiki From GQ Wiki Use RNA-Seq Workflow to measure gene expression profiles using NGS sequencing. This analysis is sometimes also referred to as Digital Gene Expression. Example use cases RNA Seq - GQ Wiki