RNOMICS

#RNA-seq analysis of single bovine blastocysts

Sat, 25 May 2013 12:16:17 +0200

Background: Use of #RNA-Seq presents unique benefits in terms of gene expression analysis because of its wide dynamic range and ability to identify functional sequence variants. This technology provides the opportunity to assay the developing embryo, but the paucity of biological material available from individual embryos has made this a challenging prospect. Results: We report here the first application of #RNA-Seq for the analysis of individual blastocysts gene expression, SNP detection, and characterization of allele specific expression (ASE). #RNA was extracted from single bovine blastocysts (n = 5), amplified, and analyzed using high-throughput sequencing. Approximately 38 million sequencing reads were generated per embryo and 9,489 known bovine genes were found to be expressed, with a high correlation of expression levels between samples (r > 0.97). Transcriptomic data was analyzed to identify SNP in expressed genes, and individual SNP were examined to characterize allele specific expression. Expressed biallelic SNP variants with allelic imbalances were observed in 473 SNP, where one allele represented between 65-95% of a variant’s transcripts. Conclusions: This study represents the first application of #RNA-seq technology in single bovine embryos allowing a representation of the embryonic transcriptome and the analysis of transcript sequence variation to describe specific allele expression. http://bit.ly/ZkjcLB #BMC

eXpress • Home

Sat, 25 May 2013 10:22:04 +0200

bio.math.berkeley.edu 200) && (this.width >= this.height) ? 200: true); max-height: 200px; height: expression((this.height > 200) && (this.height >= this.width) ? 200: true); border: none;’/> eXpress is a general quantification tool for target DNA/#RNA sequences. While its primary use currently is #RNA-Seq it has the potential for applications in many other areas including as allele-specific expression and metgenomics. What makes eXpress different is that it is an online (or streaming) algorithm, meaning it only makes one pass through the data. This allows it to be very light-weight and efficient using a constant amount of memory and time linear in the number of sequenced fragments be… posted by friends: (1) @genetics_blog: Good talk by Lior Pachter at today’s #genomics seminar. Anxiously awaiting his #rstats pkg for dif exprssn w/ http://t.co/5SuXqESg0l counts 24.05.2013 22.59.53 posted by followers of the list: (0) http://bit.ly/1aidUjd #rnomics_bioinfo

miRTCat: a comprehensive map of human and mouse micro#RNA target sites including non-canonical nucleation bulges

Sat, 25 May 2013 06:03:05 +0200

Summary: Micro#RNAs (#miRNAs) regulate various biological functions by binding hundreds of transcripts to impart post-transcriptional repression. Recently, by applying a transcriptome-wide experimental method for identifying #miRNA target sites (Ago HITS-CLIP), a novel non-canonical target site, named “nucleation bulge”, was discovered as widespread, functional and #evolutionally conserved. Although such non-canonical nucleation bulges have been proven to be predictive by using “pivot pairing rule” and sequence conservation, this approach has not been applied yet. To facilitate the functional studies of non-canonical #miRNA targets, we implement miRTCat: a comprehensive searchable map of #miRNA target sites including non-canonical nucleation bulges, not only mapped in experimentally verified #miRNA-bound regions but also predicted in all 3’ untranslated regions (3’UTRs) derived from human and mouse (~15.6% as expected false-positives).

Availability: http://ion.skku.edu/mirtcat

Contact: swchi@skku.edu

Supplementary information: Supplementary data are available at _Bioinformatics_ online. http://bit.ly/ZjPAxO #bioinformaticsj

viRome: an R package for the visualization and analysis of viral small #RNA sequence datasets

Sat, 25 May 2013 06:03:04 +0200

Summary: #RNA interference (#RNAi) is known to play an important part in defense against viruses in a range of species. Second-generation sequencing technologies allow us to assay these systems and the small #RNAs that play a key role with unprecedented depth. However, scientists need access to tools which can condense, analyse and display the resulting data. Here we present viRome, a package for R that takes aligned sequence data and produces a range of essential plots and reports.

Availability and implementation: viRome is released under the BSD license as a package for R available for both Windows and Linux http://virome.sf.net

Contact: mick.watson@roslin.ed.ac.uk

Supplementary information: Additional information and a tutorial is available on the ARK-Genomics website: http://www.ark-genomics.org/bioinformatics/virome http://bit.ly/ZjPAhy #bioinformaticsj

Structural #RNA alignment by multi-objective optimization

Sat, 25 May 2013 06:03:03 +0200

Motivation: The calculation of reliable alignments for structured #RNA is still considered as an open problem. One approach is the incorporation of secondary structure information into the optimization criteria by using a weighted sum of sequence and structure components as an objective function. As it is not clear how to choose the weighting parameters, we use multi-objective optimization to calculate a set of Pareto-optimal #RNA sequence-structure alignments. The solutions in this set then represent all possible trade-offs between the different objectives, independent of any previous weighting.

Results: We present a practical multi-objective dynamic programming algorithm, which is a new method for the calculation of the set of Pareto-optimal solutions to the pairwise #RNA sequence-structure alignment problem. In selected examples, we show the usefulness of this approach, and its advantages over state-of-the-art single-objective algorithms.

Availability and implementation: The source code of our software (ISO C++11) is freely available at http://sysbio.uni-ulm.de/?Software and is licensed under the GNU GPLv3.

Contact: hans.kestler@uni-ulm.de

Supplementary information: Supplementary data are available at _Bioinformatics_ online. http://bit.ly/1ahCQrj #bioinformaticsj

Comparative transcriptome analysis of small noncoding RNAs in different stages of Trypanosoma brucei [BIOINFORMATICS]

Sat, 25 May 2013 03:40:03 +0200

Deep-sequencing of the small RNAs in two life stages of parasitic protozoan _Trypanosoma brucei_ shows that the small RNAs can derive from various sources. Those generated from rRNAs and tRNAs are differentially expressed in the two life cycles studied. http://bit.ly/1ahilek #RNAJ

CPAT 1.2.1 - #RNA Coding Potential Assessment Tool

Fri, 24 May 2013 23:48:03 +0200

mybiosoftware.com - admin 200) && (this.width >= this.height) ? 200: true); max-height: 200px; height: expression((this.height > 200) && (this.height >= this.width) ? 200: true); border: none;’/> CPAT 1.2.1 :: DESCRIPTION CPAT (Coding Potential Assessment Tool) is a novel alignment-free method which rapidly recognizes coding and noncoding transcripts from a large pool of candidates. ::DEVELOPER Wei Li’s Computational Epigenomics Lab :: SCREENSHOTS N/A :: REQUIREMENTS Linux Python R package :: DOWNLOAD CPAT :: MORE INFORMATION Citation: Nucleic Acids Res. 2013 Apr 1;41(6):e74. doi: 10.1093/nar/gkt006. Epub 2013 Jan 17. CPAT: Coding-Potential Assessment Tool using an alignment-free logi… show all text posted by friends: (1) @biosoftcn: CPAT 1.2.1 – #RNA Coding Potential Assessment Tool http://t.co/RDvrQvqcIs 24.05.2013 11.08.41 posted by followers of the list: (0) http://bit.ly/1agG2mX #rnomics_bioinfo

RSeQC 2.3.6 - #RNA-seq Quality Control package

Fri, 24 May 2013 23:48:03 +0200

mybiosoftware.com posted by friends: (1) @biosoftcn: RSeQC 2.3.6 – #RNA-seq Quality Control package http://t.co/f2uWcWD4lI 24.05.2013 10.42.39 posted by followers of the list: (0) http://bit.ly/1agG2Dj #rnomics_bioinfo

Cenix Bioscience and Debiopharm collaborate to identify predictive biomarkers

Fri, 24 May 2013 23:15:02 +0200

Cenix BioScience a specialist in preclinical contract research and technology development in the field of ##RNAi #miRNA and high contentdriven pharmacology and Debiopharm Group Debiopharm a Switzerlandheadquartered global biopharmaceutical group of companies… http://bit.ly/ZjdHga #bioportfolio

Epigenetics and transgenerational inheritance

Fri, 24 May 2013 20:28:32 +0200

A report on the ‘Non-coding #RNA, epigenetics and transgenerational inheritance’ meeting, Churchill College, Cambridge, UK, 11-12 April 2013. http://bit.ly/ZiV2kF #BMC

Landes Bioscience

Fri, 24 May 2013 18:08:19 +0200

landesbioscience.com posted by friends: (1) @fjossinet: On the classification of long non-coding #RNAs, http://t.co/d51oFdbjTY 24.05.2013 10.15.33 posted by followers of the list: (0) http://bit.ly/ZiEjhs #rnomics_bioinfo

Long Noncoding #RNAs May Alter Chromosome's 3D Structure

Fri, 24 May 2013 18:08:18 +0200

sciencemag.org posted by friends: (1) @fjossinet: “Long Noncoding #RNAs May Alter Chromosome’s 3D Structure” http://t.co/kvPS6rS5OS 24.05.2013 10.17.02 posted by followers of the list: (0) http://bit.ly/ZiEgSS #rnomics_bioinfo

Landes Bioscience

Fri, 24 May 2013 18:08:18 +0200

landesbioscience.com posted by friends: (1) @ppgardne: #MUSTREADME: The four ingredients of single-sequence #RNA secondary structure prediction. @LandesJournals ##RNABio http://t.co/fWizij7xK6 24.05.2013 05.29.57 posted by followers of the list: (0) http://bit.ly/ZiEh9g #rnomics_bioinfo

Earth Microbiome Project - Metadata Portal

Fri, 24 May 2013 18:08:17 +0200

microbio.me posted by friends: (1) @digitalbio: The Earth Microbiome Project 16S #rRNA V4 database now up to 14,512 samples comprising 1.4 billion sequences http://t.co/LXeaMMUnmi 24.05.2013 06.48.51 posted by followers of the list: (0) http://bit.ly/ZiEjhe #rnomics_bioinfo

DNA and #RNA - Computational Medicine @ Jefferson Medical College

Fri, 24 May 2013 17:46:18 +0200

#RNomics: identification and function of small, non … Evidence for human microRNA-offset #RNAs in small #RNA sequencing data. Bioinformatics. 2009; 25(18): 2298-301 … http://bit.ly/OYFOvc #bing

Behavioral and neurogenomic transcriptome changes in wild-derived zebrafish with fluoxetine treatment

Fri, 24 May 2013 17:30:07 +0200

Background: Stress and anxiety-related behaviors are seen in many organisms. Studies have shown that in humans and other animals, treatment with selective serotonin reuptake inhibitors (e.g. fluoxetine) can reduce anxiety and anxiety-related behaviors. The efficacies and side effects, however, can vary between individuals. Fluoxetine can modulate anxiety in a stereospecific manner or with equal efficacy regardless of stereoisomer depending on the mechanism of action (e.g. serotonergic or GABAergic effects). Zebrafish are an emerging and valuable translational model for understanding human health related issues such as anxiety. In this study we present data showing the behavioral and whole brain transcriptome changes with fluoxetine treatment in wild-derived zebrafish and suggest additional molecular mechanisms of this widely-prescribed drug. Results: We used automated behavioral analyses to assess the effects of racemic and stereoisomeric fluoxetine on male wild-derived zebrafish. Both racemic and the individual isomers of fluoxetine reduced anxiety-related behaviors relative to controls and we did not observe stereospecific fluoxetine effects. Using #RNA-sequencing of the whole brain, we identified 411 genes showing differential expression with racemic fluoxetine treatment. Several neuropeptides (neuropeptide Y, isotocin, urocortin 3, prolactin) showed consistent expression patterns with the alleviation of stress and anxiety when anxiety-related behavior was reduced with fluoxetine treatment. With gene ontology and KEGG pathway analyses, we identified lipid and amino acid metabolic processes, and steroid biosynthesis among other terms to be over-enriched. Conclusion: Our results demonstrate that fluoxetine reduces anxiety-related behaviors in wild-derived zebrafish and alters their neurogenomic state. We identify two biological processes, lipid and amino acid metabolic synthesis that characterize differences in the fluoxetine treated fish. Fluoxetine may be acting on several different molecular pathways to reduce anxiety-related behaviors in wild-derived zebrafish. This study provides data that could help identify common molecular mechanisms of fluoxetine action across animal taxa. http://bit.ly/ZizaG6 #BMC

Biocenter - Innsbruck Medical University - Genomics and #RNomics

Fri, 24 May 2013 17:16:04 +0200

The division of Genomics and #RNomics is responsible for training students of the Medical … (DNA and #RNA) in particular in … Bioinformatics; Biological Chemistry … http://bit.ly/OrmSUj #bing

The Impact of Hemolysis on Cell-Free micro#RNA Biomarkers

Fri, 24 May 2013 17:14:32 +0200

The Impact of Hemolysis on Cell-Free micro#RNA Biomarkers

_— Delivered by Feed43 service_ http://bit.ly/1afwyIy #frontiers

RNA-seq Showdown

Fri, 24 May 2013 15:44:50 +0200

by Kelly Rae Chi – Biotechniques Five #RNA-seq library preparation methods go head-to-head in terms of performance in low-quality and low quantity #RNA samples. Which method came out on top? In a side-by-side comparison of five different transciptome sequencing (RNA-seq) library preparation methods, the RNase H technique outperformed others for analysis of low-quality #RNA samples […]

RNA-seq Showdown is a post from: RNA-Seq Blog http://bit.ly/1affFh8 #RNAseq

CoRAL: predicting non-coding #RNAs from small #RNA-sequencing data

Fri, 24 May 2013 15:44:49 +0200

The surprising observation that virtually the entire human genome is transcribed means we know little about the function of many emerging classes of #RNAs, except their astounding diversities. Traditional #RNA function prediction methods rely on sequence or alignment information, which are limited in their abilities to classify the various collections of non-coding #RNAs (ncRNAs). To […]

CoRAL: predicting non-coding #RNAs from small #RNA-sequencing data is a post from: RNA-Seq Blog http://bit.ly/1affEd6 #RNAseq