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.
Figures Editor: Diego Di Bernardo, Fondazione Telethon, Italy Copyright: © 2011 Costa et al. Introduction. [BioC] a few questions on DESeq. Untitled. 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 Note: the API version needs to be the same as the databases you are accessing, so please use CVS to obtain a previous version if querying older databases.
Database dumps Entire databases can be downloaded from our FTP site in a variety of formats. See our web installation instructions for full details. Each directory on ftp.ensembl.org contains a README file, explaining the directory structure. Multi-species data Single species data Showing 1 to 59 of 59 entries To facilitate storage and download all databases are GNU Zip (gzip, *.gz) compressed. About the data The following types of data dumps are available on the FTP site. FASTA sequence databases of Ensembl gene, transcript and protein model predictions. cDNA Peptides. Mozilla Firefox. 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 Below are small samples of datasets from the Illumina BodyMap 2.0 project; specifically, the datasets are paired-end 50bp reads from adrenal and brain tissues. RNA-seq data from adrenal tissue: and RNA-seq data from brain tissue: You'll also need one additional dataset: a gene annotation in GTF format. Here's a history containing all five datasets; click on the green plus to import (copy) it into your workspace.
Galaxy. Whole Transcriptome Analysis. Seq Data Analysis Tools. Data-images.Par.17842.Image.-1.0.1.gif (GIF Image, 645x442 pixels) 2010 Annual Report of the Division of Intramural Research, NICHD. 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. In the ICM, receipt of a second signal initiates transcription of gene A through attachment of a binding protein to the sign (histone modifications) put in place at the morula stage. Once transcription of gene A is underway, it can be stabilised (maintained) by other 'memory' mechanisms25 and the original sign need not be retained.
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.
Txid9913[Organism:noexp] - Nucleotide result. Bos taurus assembly. 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 . Two major releases have been made available to the public: UMD2 (April 2009)  and UMD3.0 (August 2009) . 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.