L_RNA_scaffolder: scaffolding genomes with transcripts. Sample to Sequencing RNA guide. Freshmen don’t sequence? Well, they do at William & Mary. It was the summer that the freshmen ruled the sequencer.
Technically, the six William & Mary students who logged heavy lab time with a state-of-the-art Ion Torrent gene sequencer had finished their freshman year and therefore did their summer work as rising sophomores. But never mind quibbles. Working as a group, Eileen Ablondi, Catherine Acio, Emma McGregor, Caitlin Paisley and Cheyenne Williams not only finished the sequencing of the complete genome of a human bacterial pathogen, but they also attempted RNA-Seq—a technique that sequences expressed genes—on samples from the developing nervous system of a species of frog commonly used in lab experiments. On a different front, Andrew Halleran conducted a transcriptome analysis of a “boring” bacteriophage, a virus that turned out to be not so dull, after all. And, these six students did their sequencing while holding down summer positions in other biology labs. “Sequencing a bacterial genome is not at all novel in the field,” Saha said.
Data Analysis: Today’s Next-Gen Sequencing Imperative. From Genetic Engineering News by John Russell Without question, next-generation sequencing (NGS) has been immensely successful, even if it hasn’t transformed medicine just yet.
Sequencing itself has become nearly trivial. Declining costs have made it widely accessible. Recently, the rise of affordable benchtop NGS instruments promises to democratize the technology further, extending it out from large sequencing centers into smaller labs and clinics. New RNA-Seq Library Prep Kits for Ion Torrent and SOLiD Sequencing. RNA-Seq Job Opportunities. RUCDR Infinite Biologics Selects NuGEN as Corporate Sponsor and Genomic Sample Processing Partner. PISCATAWAY, N.J.
–(BUSINESS WIRE)–RUCDR Infinite Biologics, the world’s largest university-based biorepository, has added NuGEN Technologies to its group of technology sponsors. A unit of Rutgers, The State University of New Jersey, RUCDR Infinite Biologics currently stores more than 12 million biosamples. Dr. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Featured RNA-Seq Job – SENIOR BIOINFORMATICS SPECIALIST – Tufts Technology Services.
Tufts Technology Services (TTS) is a university-wide service organization dedicated to the strategic planning, implementation, and support of technology products and services that anticipate and meet the academic, research, and business needs of the Tufts community.
TTS offers technical leadership and services to our customers with a focus on providing innovative solutions, delivering exceptional customer service, and creating a reliable infrastructure that demonstrates value to the students, faculty, staff, and alumni of Tufts University. TTS works in partnership with schools, business units, and other academic support organizations to provide campus-wide IT services in the areas of academic and research technology, enterprise application systems and services, networking and telecommunications, information security, data center operations, web services, classroom and computer lab technology, and user support, training and outreach.
Basic Requirements: Preferred Qualifications: TweeDEseq: a test for differential expression based on the Poisson-Tweedie family. RNA-Seq Blog – Poll Results. OmiRas: A Web server for differential expression analysis of miRNAs derived from small RNA-Seq data. Genohub Launches Next Generation Sequencing Marketplace. (Austin, TX – August 15, 2013 ) – Genohub Launches Next Generation Sequencing Marketplace Genohub announced the launch of their online marketplace for next generation sequencing services today.
Genohub.com announced the launch of their online market for next generation sequencing services today. The online service, is positioned to completely change the way high throughput sequencing services are ordered, accelerating genomic research by improving access to sequencing services. Genohub’s intelligent sequencing matching engine instantly matches researchers with service providers based on specific project criteria. GobyWeb: Simplified Management and Analysis of Gene Expression and DNA Methylation Sequencing Data. A powerful strategy for developing microbial cell factories by employing synthetic small RNAs. August 09, 2013The current systems for the production of chemicals, fuels and materials heavily rely on the use of fossil resources.
Due to the increasing concerns on climate change and other environmental problems, however, there has been much interest in developing biorefineries for the production of such chemicals, fuels and materials from renewable resources. For the biorefineries to be competitive with the traditional fossil resource-based refineries, development of high performance microorganisms is the most important as it will affect the overall economics of the process most significantly. Metabolic engineering, which can be defined as purposeful modification of cellular metabolic and regulatory networks with an aim to improve the production of a desired product, has been successfully employed to improve the performance of the cell.
However, it is not trivial to engineer the cellular metabolism and regulatory circuits in the cell due to their high complexity. Dr. Identify and visualize expressed transcripts in RNA-Seq data using GenomeSpace. Roche launches GS FLX+ System software update to extend read lengths for targeted gene sequencing and microbial community profiling studies. The latest Software Version 2.9 enables highly accurate sequencing of long 16S ribosomal RNA amplicons for more precise taxonomic assignment of organisms in microbial surveys.
Penzberg, Germany and Branford, CT, USA – August 6, 2013 Roche announced today the global launch of a new software update that significantly extends the range of amplicon lengths available for targeted next-generation sequencing studies on the 454 GS FLX+ System. The latest software enables sequencing of amplicons up to 800 bp while maintaining >99% accuracy over the length of the read. High quality sequencing of even longer amplicons up to 1,100 bp has been successfully demonstrated in early access testing. The long read improvements allow researchers to obtain more complete coverage of target gene regions using fewer amplicons, both simplifying experimental design and improving the biological relevance of sequencing results.
Fluidigm Enables the Study of miRNA Master Regulators Down to the Single Cell Level. SOUTH SAN FRANCISCO, Calif.
–(BUSINESS WIRE)–Fluidigm today announced it has added microRNA (miRNA) Expression Profiling to its C1TM Single-Cell Auto Prep System, providing the ability to unlock the secrets of miRNA in single cells. The new protocol equips researchers with the simplest, fastest and most flexible workflow available to co-amplify hundreds of miRNAs in an individual cell while processing up to 96 cells in parallel. TruHMM: an algorithm for assembling full-length transcripts in prokaryotes using directional RNA-Seq short reads. Aug August 5, 2013 | Leave a Comment Although RNA-seq has become the major method for analyzing the complexity of prokaryotic transcriptome, it is still a challenging task to accurately assemble full length transcripts using short RNA-seq reads. Researchers from the University of North Carolina at Charlotte have profiled the transcriptomes of E. coli K12 under different culture conditions and growth phases using a highly specific directional RNA-seq technique that can capture various types of transcripts in the bacterial cells, combined with a highly accurate and robust algorithm and tool TruHMM for assembling full length transcripts.
They found that 46.9 ~ 63.4% of expressed operons were utilized in their putative alternative forms, 72.23 ~ 89.54% genes had putative asRNA transcripts and 51.37 ~ 72.74% intergenic regions had putative ncRNA transcripts under different culture conditions and growth phases. Availability – TruHMM is available at Incoming search terms: Featured RNA-Seq Jobs. UCLA and Chinese scientists analyze genetic makeup of human and mouse embryos in unprecedented detail. Single-cell RNA sequencing could lead to improved diagnoses of genetic diseases By Shaun Mason July 30, 2013 UCLA scientists, in collaboration with teams in China, have used the powerful technology of single-cell RNA sequencing to track the genetic development of a human and a mouse embryo at an unprecedented level of accuracy.
The technique could lead to earlier and more accurate diagnoses of genetic diseases, even when the embryo consists of only eight cells. The study was led by Guoping Fan, professor of human genetics and molecular biology and member of both the Jonsson Comprehensive Cancer Center and the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research. The findings were published in the online edition of the journal Nature and will appear later in the print edition. Single-cell RNA sequencing allows researchers to determine the precise nature of the total gene transcripts, or all of the genes that are actively expressed in a particular cell.
A Beginner’s Glance at RNA sequencing vs. Exome sequencing. Contributed by a reader As with all novel technologies that are becoming mainstream in research labs, a scientist coming into any new field might find themselves inundated with all of the available options for what they need to do.
This is certainly the case with next generation sequencing technologies. The field is rapidly increasing with new tools for different approaches to sequencing being made available every day. In the case of analyzing the expression profile for a particular sample, exome sequencing and RNA sequencing are two very useful applications. However, each provides different information which is not readily apparent, and making the decision as to which tool to use isn’t either. Exploring DNA/RNA-Seq Analysis Results with Golden Helix GenomeBrowse and SVS. UT San Antonio Scientist Among Researchers Investigating the Transcriptome. From BioNewsTexas To date, developments in DNA sequencing have provided high-quality and high-confidence genetic and genomic data.
However, more information is needed to characterize biological systems beyond DNA information. Researchers are currently using RNA-Seq which is a deep-sequencing technique to profile the transcriptome. SBIR grant hones DNASTAR software for clinical research. A Small Business Innovation Research (SBIR) grant from the US National Institutes of Health (NIH) has set DNASTAR on the next stage of expanding its sequence assembly and analysis software from general research usage to the clinical-research market.
A lifescience software company based in Madison, Wisconsin, DNASTAR started off developing and marketing desk-top software for DNA and protein sequence assembly and analysis. It has since broadened its offering to include next-generation sequencing applications such as RNA-Seq and ChIP-Seq, as well as microarray gene-expression software. Phase II The Phase II SBIR grant award from the NIH is for a project called ‘Association Analysis Software for Mining Clinical Next-Gen Sequencing Data’. This is the second phase of a programme initially funded in 2012, DNASTAR explained. The value of the grant was not disclosed, although SBIR Phase II awards from the NIH normally do not cover more than total costs of US$1,000,000 over a two-year period.
Hands-on Tutorial: RNA-seq Analysis using Cluster Computing. Small RNA Read Alignment for Accurate Quantification. Vamsi Veeramachaneni, Strand Life Sciences Pvt. Ltd. There are two common methods for aligning small RNA reads (after we take care of such pesky details as trimming the adapters). We can create a reference collection of known small RNA sequences and align the reads against this collection, orwe could align the reads against the entire genome and use genome-based annotations to later compute small RNA gene expression Both methods have their own pros and cons. Alignment against the genome can be tricky because of the number of parameters that need to be specified to the alignment tool. Minimum quality of alignment: specified as the number (or %) of mismatches/gaps that can be tolerated,Number of matches allowed: for reads which match in more locations than this threshold, we can either choose to report a random subset of the matches or ignore the read entirely.
We were of course curious about the nature of the reads aligning to the genome with such high multiplicity. Analysis of RNA‐Seq Data. RNA – Seq data analysis. Comparative analysis of RNA – Seq data with DESeq and DEXSeq. RNA seq and splicing analysis. New study reveals important role of insulin in making breast milk. Why do so many mothers have difficulty making enough milk to breastfeed? A new study by scientists at Cincinnati Children’s Hospital Medical Center and the University of California Davis adds to their previous research implicating insulin’s role in lactation success. The study is the first to describe how the human mammary gland becomes highly sensitive to insulin during lactation. It is also the first study to get an accurate picture of how specific genes are switched on in the human mammary gland during lactation. The researchers used next generation sequencing technology, RNA sequencing, to reveal “in exquisite detail” the blueprint for making milk in the human mammary gland, according to Laurie Nommsen-Rivers, PhD, a scientist at Cincinnati Children’s and corresponding author of the study, published online in PLOS ONE, a journal of the Public Library of Science.
Dr. This approach revealed a highly sensitive portrait of the genes being expressed in human milk-making cells. Dr. Zebra fish RNA-Seq PE TopHat read alignment and CuffLink assembly. Post-transcriptional activation of a diguanyla... [Mol Microbiol. 2013. RNA-Seq Reveals Antarctic Lake Teems With Life.
From The Scientist by Chris Palmer In an environment most scientists thought was so completely inhospitable to life that it was once considered a model for other planets, scientists have unearthed a vast web of organisms. RNA-Seq Blog – Poll Results. The 2013 RNA-Seq Workshop: From Pipette to P-value! Postdoctoral Position in Bioinformatics and RNA-seq Analysis. RNA-Seq Blog. RNA-Seq Interactive Literature Review.
Science Gone Social. By Tracy Vence at Genetic Engineering News.com From keeping up with the literature to sparking collaborations and finding funds, scientists are storming social media. Not many scientists have produced manuscripts as a direct result of participating in discussions on social media. Fewer still support their research programs in full by funds obtained in the same way. But, respectively speaking, Emily Darling, Ph.D., and Karthik Ram, Ph.D., attribute these outcomes to their activities on Twitter. Drs. Twitter, says Aaron Darling, Ph.D., “is an exceptionally efficient way to communicate about science, whether it’s carefully vetted results or wild ideas.”
Next Generation Sequencing Market NGS – Pre-Sequencing, Cloud Computing & NGS Bioinformatics Solutions are Growth Opportunities Says New Research Report at ReportsnReport. “Next Generation Sequencing (NGS) Market [Platforms (Illumina HiSeq, MiSeq, Life Technologies Ion Proton/PGM, 454 Roche), Bioinformatics (RNA-Seq, ChIP-Seq), (Pyrosequencing, SBS, SMRT), (Diagnostics, Personalized Medicine)] – Global Forecast to 2017” is the new market research report added to ReportsnReports.com store. An Appliance Built Exclusively for Galaxy.
July 1, 2013 | Galaxy, the well-loved open source tool for data-intensive biomedical research, is getting some new gear. At the Galaxy User Group meeting in Oslo, Norway, BioTeam announced a new hardware appliance specifically for Galaxy: the SlipStream Appliance: Galaxy Edition. According to the agreement with the Galaxy Project, for the next two years BioTeam will be the exclusive appliance vendor for Galaxy.
RNASeq. Resources.