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Helicos BioSciences Corporation has now named all three major competitors in a lawsuit claiming willfull infringement on their patents which broadly cover sequencing-by-synthesis technology.  They claim that Pacific Biosciences, Life Technologies, and Illumina have all incorporated Helicos’ patented technology “at the heart of” their respective sequencing systems and products.

The patents cover sequencing-by-synthesis methods using labeled nucleotides. The nucleotides are labeled with detectable markers, such as fluorescent markers, that enable determination of each nucleotide incorporated into the DNA strand being extended by the polymerase. The patents describe processes that involve, for example, identifying each new nucleotide by observing its detectable label and neutralizing or removing the label before addition of the next nucleotide. The specific claims apply to both “real time” and “step and repeat” approaches.

“After a careful examination of the sequencing products and technologies offered by Illumina and Life Technologies, we are convinced that they, in addition to Pacific Biosciences, infringe the Helicos patents, which are in full force and effect up through 2028,” stated Dr. Ivan Trifunovich, President and CEO of Helicos.

Recently, Helicos had stated a strategic initiative to vigorously protect their next-generation sequencing IP.

(Read the press release… )

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New RNA-Seq methods give us the ability to comprehensively and accurately assess the levels of the entire repertoire of miRNAs (including all sequence variants) in a given sample.

Researchers at the Institute for Systems Biology have conducted a comprehensive survey of microRNA isomiRs from human and mouse samples using next generation sequencing platforms and constructed a database that catalogs all microRNA isomiRs. Read more

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from GenomeWeb By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – A new small RNA sequencing study is providing insights into how some jawless vertebrate animals called the agnathans are related to one another and to jawed vertebrates, known as gnathostomes.

A team of researchers from the US, UK, and France used high-throughput sequencing to look at the small RNA repertoire in hagfish and lamprey specimens, comparing these patterns to those found in jawed vertebrates. The research, scheduled to appear online this week in the Proceedings of the National Academy of Sciences, suggests that the present day jawless vertebrates, known as cyclostomes because of their round mouths, may belong to a single evolutionary lineage rather than arising from parallel lineages. (read more… )

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Next Generation Sequencing Transcriptome Assembly Workshop

01 November, 10 09:00 AM – 02 November, 10 01:00 PM

e-Science Institute, 15 South College Street, Edinburgh

Organiser: Mark Blaxter

A major output from the current generation of high throughput sequencers is transcriptomes. The transcriptome (all the RNAs produced by a cell or organism) represents the biological distillation of the genome, and is often a very useful way in which to investigate biology. Correct assembly of a transcriptome from the short sequence reads is an essential first step in further analysis, but there is still no consensus of best practice or optimality goals.

The Next generation Transcriptome Assembly Workshop is aimed at practising bioinformaticians and biologists who want o explore the options for assembling de novo the transcriptomes of new species using only next generation, short and long read data. We will examine the properties of the sequence data being produced, and review the available algorithms and packages that can be used for assembly. We will aim to produce a series of best-practice recommendations for the future application of these technologies to gene discovery and assembly.

Workshop webpage – http://www.nesc.ac.uk/esi/events/1104/

e-Science Institute homepage – http://www.esi.ac.uk/

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10/14/2010 – UC Davis Researchers Using CLC bio for Cutting-Edge RNA-Seq Milk Cell Transcriptome Publication

DAVIS, Calif.–(BUSINESS WIRE)–Researchers from the Department of Animal Science at UC Davis are using RNA-seq technology and data analysis software from CLC bio to develop the first comprehensive description of the bovine milk and mammary gland transcriptome in lactating cows. The results reveal that approximately 50% of the annotated genes are expressed during lactation and that variations in gene expression exist at different stages of lactation as an adaptation to different molecular functions of milk according to the biological need of the animal. (read the entire release… )

10/12/2010 – Illumina to Announce Third Quarter 2010 Financial Results on Tuesday, October 26, 2010

SAN DIEGO–(BUSINESS WIRE)–Illumina, Inc. (NASDAQ:ILMN) today announced that it will issue results for third quarter 2010 following the close of market on Tuesday, October 26, 2010.

On the same day, at 2:30pm Pacific Time (5:30pm Eastern Time), Jay Flatley, President and Chief Executive Officer, and Christian Henry, Senior Vice President, Chief Financial Officer, and General Manager, Life Sciences, will host a conference call with analysts, investors, and other interested parties to discuss financial and operating results. (read the entire release… )

10/05/2010 – Strand Releases Avadis NGS Software to Enable Biologists to Analyze Next-Generation Sequence Data

SAN FRANCISCO–(BUSINESS WIRE)–Strand Scientific Intelligence, Inc. (Strand) today announced the worldwide release of Avadis NGS, a software application for next-generation sequence (NGS) analysis. Avadis NGS helps biologists visualize and perform downstream analysis on their NGS data, simply on a desktop computer.

Avadis NGS is an application focused on ChIP-SEQ, RNA-SEQ and genetic variation analysis that enables its users to assimilate large amounts of NGS data and ascertain deep biological insights using powerful statistics, interactive data visualizations in a state-of-the-art genome browser, and downstream analyses such as GO, pathways and GSEA. (read the entire release… )

More than half of survey respondents said they are using NGS for RNA-Seq applications.

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For species that lack reference genome sequences, or whose genomes are poorly annotated, de novo short-read transcriptome assembly may be a practical alternative to conventional expressed sequence tag–based approaches and to methods that depend on short-read alignments. Read more

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• USING TRANS-ABYSS TO MERGE ASSEMBLIES

Thanks to the new technological advances in genome and transcriptome sequencing, we know that a major portion of the genome is being transcribed but only a small portion of this transcriptome contains the protein-coding sequences. The remainder can be split (at approximately 100 nucleotide length) into two major categories: small non-coding RNA (including microRNA) and long non-coding RNA, both of which have been shown to exert regulatory control over protein production/expression. 

Interestingly, these two types of non-coding RNA exert their control by very different mechanisms.  Small RNAs regulate gene expression predominantly through reduction of mRNA levels and subsequent reduced protein output¹ (negative regulation), while long non-coding RNAs increase the synthesis of nearby proteins² (positive regulation).

(read more about negative regulation by small non-coding RNAs… )

(read more about positive regulation by long non-coding RNAs… ) 

1. Guo H, Ingolia NT, Weissman JS, Bartel DP. (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466(7308), 835-40. [abstract]
2. Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, Guigo R, Shiekhattar R. (2010) Long Noncoding RNAs with Enhancer-like Function in Human Cells. Cell143(1), 46-58. [abstract]

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• SEQanswers – RNA Sequencing

  • reason for low mapping rate?? May 23, 2013
    we did RNASeq using HiSeq 2000 100PE. When the data were back, I mapping them to the reference sequence, but got very low mapping rate (30-40%). I... […]
    miaom
  • cross-species data - questions about normalization May 23, 2013
    Hi, I have some data form various samples (cell types) in different species. I want to compare and analyze gene expression variability across the... […]
    trelek2
  • CuffDiff strange output May 23, 2013
    Hi, I hope that someone can be so gentle to help me. I'm analizing some data from RNA-Seq with TopHat and Cufflinks and I focus my attention on... […]
    Pruexel
  • cannot away with cuffdiff,incredible May 23, 2013
    Hi,all I have 4(A,B,C,D) sample in 4 times(increasing time),I got diff result in 3 different cuffdiff 1.cuffdiff 3(A,B,C) individual... […]
    upper
  • TopHat extremely low paired mapping rate. PLS HELP! May 22, 2013
    Hey 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, 2013
    Hi 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

• 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 data
    I 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 […]