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Jun
29
RNA-Seq – A Status Update
Filed Under Information, Publications | Leave a Comment
Hybridization- and tag-based technologies have elucidated the involvement of multiple genes and pathways in pathological conditions, providing insights into the expression of thousand of coding and noncoding RNAs, such as microRNAs. However, the introduction of Next-Generation Sequencing, particularly of RNA-Seq, has overcome some drawbacks of previously used technologies.
Identifying, in a single experiment, potentially novel genes/exons and splice isoforms, RNA editing, fusion transcripts and allele-specific expression are some of its advantages.
RNA-Seq has been fruitfully applied to study cancer and host-pathogens interactions, and it is taking first steps for studying neurodegenerative diseases (ND) as well as neuropsychiatric diseases. In addition, it is emerging as a very powerful tool to study quantitative trait loci associated with gene expression in complex diseases. This paper provides an overview on gene expression profiling of complex diseases, with emphasis on RNA-Seq, its advantages over conventional technologies for studying cancer and ND, and its limitations.
- Costa V, Aprile M, Esposito R, Ciccodicola A. (2012) RNA-Seq and human complex diseases: recent accomplishments and future perspectives. Eur J Hum Genet [Epub ahead of print]. [abstract]
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Jun
28
The fish-hunting cone snail, Conus geographus, is the deadliest snail on earth. In the absence of medical intervention, 70% of human stinging cases are fatal. Although, its venom is known to consist of a cocktail of small peptides targeting different ion-channels and receptors, the bulk of its venom constituents, their sites of manufacture, relative abundances and how they function collectively in envenomation has remained unknown.
Researchers at the University of Utah have used RNA-Seq to systemically elucidate the contents the C.geographus venom duct, dividing it into four segments in order to investigate each segment’s mRNA contents. Three different types of Calcium channel (each targeted by unrelated, entirely distinct venom peptides) and at least two different nicotinic receptors appear to be targeted by the venom. Moreover, the most highly expressed venom component is not paralytic, but causes sensory disorientation and is expressed in a different segment of the venom duct from venoms believed to cause sensory disruption. They have also identified several new toxins of interest for pharmaceutical and neuroscience research.
This transcriptome analysis provides a new physiological framework for understanding the molecular envenomation strategy of this deadly snail.
- Hu H,Bandyopadhyay PK, Olivera BM, Yandell M. (2012) Elucidation of the molecular envenomation strategy of the cone snail conus geographus through transcriptome sequencing of its venom duct. BMC Genomics 13:284. [article]
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Jun
27
Bellerophontes – a fully automated framework for the detection of novel fusion transcripts in paired end RNA-Seq data
Filed Under Splicing and Junction Mapping | Leave a Comment
Bellerophontes is a new framework for the detection of fusion transcripts through short paired-end reads which integrates splicing-driven alignment and abundance estimation analysis, producing a more accurate set of reads supporting the junction discovery and taking into account also not annotated transcripts. Bellerophontes performs a selection of putative junctions on the basis of a match to an accurate gene fusion model. Bellerophontes runs on top of TopHat and Cufflinks tools (developed by Trapnell et al.). The analysis is based on the results of TopHat alignment and Cufflinks transcript isoform detection.
AVAILABILITY: Bellerophontes JAVA/Perl/Bash software implementation is free and available at http://eda.polito.it/bellerophontes/
- Abate F, Acquaviva A, Paciello G, Ficarra E, Ferrarini A, Delledonne M, Soverini S, Martinelli G, Macii E. (2102) Bellerophontes: A RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model. Bioinformatics [Epub ahead of print]. [abstract]
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Jun
27
NorahDesk – a small non-coding RNA (ncRNA) detection tool for RNA sequencing (RNA-Seq) data
Filed Under Other Tools | Leave a Comment
NorahDesk reconstructs full-length putative ncRNA transcripts from short sequence reads by hybridizing contigs. It analyzes not only the distinct read distribution of true ncRNA classes in an unbiased way but also utilizes secondary structures as an independent confirmation source to reliably predict ncRNA from deep sequencing data.
Using publicly available mouse sequence data from brain, skeletal muscle, testis and ovary, NorahDesk was evaluated with an emphasis on the performance for microRNAs (miRNAs) and piwi-interacting small RNA (piRNA). This method was also compared with Dario and mirDeep2 and found to produce longer transcripts with higher read coverage. This feature makes it the first method particularly suitable for the prediction of both known and novel piRNAs.
NorahDesk and the mouse small ncRNA annotation file in BED format used in this study are available at http://www.bioinformatics.org.au/NorahDesk.
- Ragan C, Mowry BJ, Bauer DC. (2012) Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data. Nucleic Acids Res [Epub ahead of print]. [article]
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Jun
26
Dissect – a novel transcriptome-to-genome alignment tool
Filed Under Splicing and Junction Mapping, Transcriptome Assembly Tools | Leave a Comment
Dissect (DIScovery of Structural Alteration Event Containing Transcripts), a novel transcriptome-to-genome alignment tool, can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions. Dissect is suitable for whole transcriptome structural variation discovery problems involving sufficiently long reads or accurately assembled contigs.
Dissect was tested on simulated transcripts altered via structural events, as well as assembled RNA-Seq contigs from human prostate cancer cell line C4-2. AVAILABILITY:
Dissect is available for public use at: http://dissect-trans.sourceforge.net
Yorukoglu D, Hach F, Swanson L, Collins CC, Birol I, Sahinalp SC. (2012) Dissect: detection and characterization of novel structural alterations in transcribed sequences. Bioinformatics 28(12):i179-i187. [article]
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Jun
26
Xenome – A tool for classifying reads from xenograft samples
Filed Under Other Tools | Leave a Comment
Xenome performs fast, accurate and specific classification of xenograft-derived sequence read data. It has been evaluated on RNA-Seq data from human, mouse and human-in-mouse xenograft datasets.
Availability: Xenome is available for non-commercial use from http://www.genomics.csse.unimelb.edu.au/product-xenome.php
Conway T, Wazny J, Bromage A, Tymms M, Sooraj D, Williams ED, Beresford-Smith B. (2012) Xenome–a tool for classifying reads from xenograft samples. Bioinformatics 28(12): i172-i178. [article]
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Jun
25
from Genetic Engineering News
Instead of one gene or protein, the new paradigm in cancer research focuses on the analysis of entire sets of genes and proteins to identify drug targets. Multiple experimental and data analysis methodologies are being used to achieve this goal, and new bioinformatics tools will advance successful research efforts.
The availability of array-based gene profiling to yield cancer gene-expression signatures has already impacted clinical decision making in several cancers. Known types and subtypes of cancers can be distinguished by gene-expression patterns, and new molecular subtypes of cancer have been discovered that are associated with a propensity to metastasize and sensitivity or resistance to particular therapies.
While researchers have been using DNA microarrays to yield information about the molecular heterogeneity of cancer, analyses that evaluate cancer transcriptome information alongside other data will be able to extract deeper biological insights. The idea is to look at cancer interaction networks and understand regulatory mechanisms encoded in cancer gene expression. Read more
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Jun
22
Beta Testers Wanted – New RNA-Seq Data Analysis Software
Filed Under Data Analysis, Expression and Quantification, Reader Conributions | Leave a Comment
The Ingenuity iReport team is currently developing features for the analysis and interpretation of human RNA-Seq isoform-specific data. They are adding functionality to support the visualization and interpretation of isoform-specific expression data and need your help making sure these new features will enable researchers to get the most out of their data.
If you have human RNA-Seq isoform-level data and are interested in participating in their beta program, please contact Megan Laurance directly at mlaurance@ingenuity.com for more details.
Additionally, you can check out how iReport is helping biologists understand their RNA-Seq data at the gene-level today by following this link: https://apps.ingenuity.com/ireport/d…t?reportid=593
Jun
22
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Jun
20
The Breast Cancer Landscape
Filed Under Publications | Leave a Comment
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients.
A team led by researchers at the University of Cambridge, UK performed an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (copy number variants and single nucleotide polymorphisms) and acquired somatic copy number aberrations (CNAs) were associated with expression in ~40% of genes, with the landscape dominated by cis- and trans-acting CNAs. (read more…)
- Curtis C et al. (2012) The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature [Epub ahead of print]. [article]
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Jun
19
RNA Seq of Listeria monocytogenes
Filed Under Presentations | Leave a Comment
Dr. Torsten Hain, Justus-Liebig-University Giessen, Germany
Dr. Hain and his coworkers have used the Ion Torrent PGM™ platform to sequence small non coding RNAs in Listeria monocytogenes in a study aimed to develop new therapeutic approaches
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Jun
19
The Allen Institute for Brain Science creates broad and useful data and analysis tools for the scientific community. The Scientist, RNA-seq Technology Development, brings scientific and technical expertise to a new initiative at the Allen Institute to understand the information networks within cells. The goals of the Molecular Networks project are: 1) to build a comprehensive multimodal tool and “Omics” dataset to dynamically describe the trajectory of human stem cells as they differentiate into neurons; 2) to use the developed tools and data sets to understand cognitive disorders. The scientist is an essential part of the team responsible for the Molecular Networks project. He/she will be the project expert on the cutting edge molecular biology techniques and be responsible to generate a strategy to uniquely read out a cells transcriptional history via nucleic acid barcodes. This individual has deep experience next-generation sequencing technology including; RNA-seq library construction, Illumina Hiseq and Miseq platforms and downstream data processing and analysis. He/she will leverage their existing creativity and technical expertise to further the goals of the Molecular Networks project. (read more…)
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Jun
15
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SEQanswers – RNA Sequencing- TopHat extremely low paired mapping rate. PLS HELP! May 22, 2013Hey guys, I have some problems with my paried-end RNA seq analysis on Galaxy. As you can see in the bam flagstat output, my tophat alignment rate is... […]Felix.Lee
- Identifying small RNA sequence within whole genome sequence May 21, 2013Hi all, I want to know if there are any useful bioinformatic tool to find small RNA sequence within a whole bacteria genome. Thank you in... […]Inma
- standard of clean data May 21, 2013Hi all I recently got my prokaryotes RNA-seq data report back. the standard filter steps of the raw data set by our local sequencing center is as... […]Pengfei Liu
- Problem with cummeRbund diffData() May 20, 2013Hi all, I'm running Tophat/cufflinks/cuffdiff for differential gene expression and analysis with cummeRbund (v 2.0.0). I'm having an issue with... […]Enrique Zudaire
- How to increase rowsize in heatmap? May 16, 2013Hi, I am a complete newbie to all things cummeRbund and am currently fighting with generating readable heatmaps. When I use ... […]Mags
- novoalign mapping May 15, 2013Hi, I want to use novoalign to map reads - allowing up to 15 mismatches for 100 bp paired-end reads I am new to novoalign(went through the... […]abh
- TopHat extremely low paired mapping rate. PLS HELP! May 22, 2013
- Biostar – RNA-Seq
- Why am I getting so many unmapped reads in STAR, classified as "too short"?I am currently using STAR to map several Hi-SEQ mRNA runs. I'm having trouble getting a decent amount of reads to map, but I don't really understand why. I'm hoping you can shed some light :) In the final log, only about 50% (or less) of the reads map to the reference. I'm using a GTF in addition to the genome. The unmapped bin that most […]
- What are the best practices for SNP identification in RNA seq transcriptome dataI have 20 RICE RNA seq tranascriptome data hiseq 2000 platform paired end reads. I aligned fasta reads with BWA and remove PCR duplicates with PICARD. Later I call SNP with samtools using various parameters. I would like to clarify what parameters should I used while alinging to reference rice genome for looking SNP location 100 bp upstream and 250 bp downst […]
- How do TopHat options -g , --supress-hits, and Bowtie options interplay?Hi, I am currently using TopHat2 to map RNA-seq runs. I think there have been some changes pertaining the -g option. Does anyone know how it works now? I used to think that setting -g would look for n alignments for a given read, report them [if top-scoring] and discard those reads that had more than g [top scoring] alignments. Now, the description sounds mo […]
- What happened to -k in TopHat for multiple-mapping reads?Selecting -g n in tophat does not discard reads mapping more than n, but instead only reports n alignments for those out all all their TOP scoring alignments. I think there used to be an option -k that would allow one to discard reads that topped x alignments -- whatever happened to that? I only see -g in the tophat 2 manual, no reporting options like before […]
- Does tophat use the library-type information for mapping, or just for the XS flag?When I specify library-type to TopHat, i.e., first-strand, second-strand, unstranded, TopHat appends a value + or - to the XS:A flag, which is useful for subsequent analyses, such as annotation. However, does this information actually influence the "mappability" of reads, or is this unaffected? My thinking is that the information would be considere […]
- Purpose of Y-shaped adapters in Illumina Sequencing?Hi all, Y adapters different sequences to be annealed to the 5' and 3' ends of each molecule in a library. The arms of the Y are unique, and the middle part, connected to the DNA fragment, is complementary. What are the advantages of this? My take of this over having fully-complementary adapters (ADAPTER1 - - - - - ADAPTER1) is that: -Upon primer a […]
- Why am I getting so many unmapped reads in STAR, classified as "too short"?