26/08/11: Reminder – Upcoming Agilent Genomics eSeminars
August 26, 2011 by Peter · Leave a Comment
Link to Agilent’s registration page for these eSeminars is here.
Example subjects include CytoGenomics and Whole Exome Sequencing
23/08/11: New SureSelect Brochure and Educational Website Launched
August 23, 2011 by Peter · Leave a Comment
SureSelect has a new brochure and educational website, so without further ado, here they are:
1. New SureSelect Brochure. This new piece goes through the SureSelect product portfolio, at the same time highlighting all key SureSelect benefits.
2. New SureSelect Educational Website. The key goals of the new website are to help educate researchers on SureSelect and to help customers easily find support and sales documents. In the Educational website, you will find videos, webinars, publications, manuals/protocols, etc.
Select the DNA you need for your Next Generation Sequencing Project
16/08/11: Agilent Launch their SureScan Microarray Scanner!
August 16, 2011 by Peter · Leave a Comment
This is from Agilent’s press release of yesterday. Sounds pretty good (if you don’t want to read the corporate stuff, skip to the bottom of this post to find a couple of information sheets, as well as a picture of the new instrument):
Agilent today introduced the SureScan Microarray Scanner, the latest innovation in scanner technology and the foundation of Agilent’s complete microarray solution for both gene expression and CGH/cytogenetics research applications.
The new SureScan system delivers the highest sensitivity, widest dynamic range and exceptional resolution, providing researchers with the greatest degree of confidence in their microarray results.
In addition, the manufacturing process used on the SureScan Microarray Scanner is ISO 13485 certified, demonstrating Agilent’s commitment in assuring controlled processes.
The SureScan system offers a streamlined workflow, allowing researchers to continuously load microarray slides while the instrument is operating. With the system’s random scanning capability, they can also reprioritize and rearrange the scan queue order at any point during the operation.
Raw image data is automatically loaded into Agilent Feature Extraction software, eliminating manual transfer.
The compact Agilent SureScan Microarray Scanner (16.5 in. high, 17 in. wide and 26 in. deep) conserves bench space. The system also combines a newly designed slide cover and a built-in ozone barrier system to minimize dye signal degradation, protecting valuable samples.
Extremely sensitive results are achieved by the unique dynamic autofocus mechanism in conjunction with a detection limit of as low as 0.01 fluorophores per square micron. These enable users to capture quality data from samples with both low and high signals.
“Researchers can be confident that the new SureScan system will deliver consistently good microarray results for many years to come,” said Robert Schueren, Agilent vice president and general manager, Genomics. “With our market-leading portfolio of microarrays, custom microarrays, reagents and software, our customers can invest in one platform knowing that it will fit a wide range of research needs.”
As promised, here are two PDF files that give a nice overview of the SureScan Microarray Scanner and how you can get the best use out of it!
1. Surescan Microarray Scanner Technical Data Sheet
15/08/11: Agilent Bioreagent and SureCycler Promotion (Denmark only)
August 15, 2011 by Peter · Leave a Comment
How nice: promotion that is specific to researchers in Denmark! In summary, you get the following great offer:
Promotional offer on StrataClone PCR Cloning kits, Competent Cells and Quikchange Lightning Mutagenesis kits (PDF file)
- Receive a 20% discount on StrataClone PCR Cloning Kit
- Buy 3 packs of competent cells receive your cheapest pack for free (this can be any competent cell)
- Receive a 20% discount on QuikChange Lightning kits
Order Promo Code: 1106_QCL. Offers ends October 31, 2011
On the flyer you will see mention of Agilent’s new 8800 SureCycler PCR Instrument and 30% discount, if you purchase any bioreagent using the above offers.
11/08/11: Looking for a “Model Organism” SureSelect All Exome Kit?
August 11, 2011 by Peter · Leave a Comment
This is just a short email and “shout out” to those researchers who are doing next-gen sequencing on model organisms and are interested in Agilent’s SureSelect targeted sequencing product. Please contact me – I might well be able to help you!
06/08/11: Specialists at Macrogen Discovered Extensive Genomic and Transcriptional Diversity
August 6, 2011 by Peter · Leave a Comment
Sequencing Specialists at Macrogen with Korean and US Scientists Discovered Extensive Genomic and Transcriptional Diversity through Massively- Parallel DNA and RNA sequencing
In a paper published in the online edition of Nature Genetics on July 3, 2011, sequencing specialists and scientists from Macrogen Inc., Axeq Technologies, Psoma Therapeutics Inc., Brigham and Women’s Hospital and Harvard Medical School reported the discovery of a wide range of novel genetic variants based on the deep sequencing of 18 genomes and 17 transcriptomes of unrelated Korean individuals.
The analysis of the genomic and transcriptomic data enabled the identifications of 9.56 million genomic variants, 23.2% of which appear to be previously unidentified, and 4,414 novel transcripts.
When comparing the genomic and transcriptomic data, 1,809 sites of transcriptional base modifications were detected, where the transcriptional landscape is different from the corresponding genomic sequences. Approximately 90% of these modifications were located in untranslated regions, suggesting potential functional roles in modifying mRNA stability.
“We identified a considerable number of new variants and found that many rare putative functional variants likely remain to be identified despite majorefforts in recent years to catalog human genomic variation. Indeed, our findings suggest that a substantial number of Korean common functional variants may not be tagged well by neighboring ‘tagging’SNPs on microarrays. These results suggest that many association studies may have fundamental limitations, especially for populations that were not included in the initial LD*assessments on the human genome ” said Jeong-Sun Seo, chairman of Macrogen and professor of medicine at the Seoul National University.
With the experience gained from the analysis of the massive genomic and transcriptomic data, Macrogen scientists have also concluded the following findings that could benefit researchers in their designs of sequencing strategies-
. Increased lengths of sequencing reads are highly advantageous for short indel detections
. Low-coverage sequencing may miss short indels despite longer read length, especially for heterozygous indels
. Copy number deletions can be detected accurately using whole-genome sequencing, especially if data from multiple genomes can be compared.
. Increased read length of short reads improved efficiency for identification of exact breakpoints in large deletions
. Because the ability to capture structural variants by whole-genome sequencing is still limited, most of the structural variants discovered in this study were large deletions (size >1 kb) and are located at relatively ‘easily accessible regions’ of the human genome.
. Sequencing with high-coverage and longer DNA reads is necessary for specific structural variations such as smaller deletions (50500 bp), copy number gains, DNA insertions and inversions.
Macrogen specializes in a wide variety of DNA / RNAsequencing applications, and offers both sequencing and data analysis services. The same Macrogen’s sequencing team that generated the data for this Nature Genetics article will handle all clients’ projects.
To see the abstract of the publication and the related article, please visit website links below:
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.872.html
Source: Nature Genetics Article preview
http://www.genomeweb.com/sequencing/sequencing-study-explores-genetic-variation-korean-population
Source: GenomeWeb News Daily News Nature
05/08/11: EnBase is now available for Yeast Biotransformations
August 5, 2011 by Peter · Leave a Comment
It is now possible to use EnBase to obtain high cell densities and the ability to have effective growth in small cultures of yeast! This is great news and reflects the hard work that the BioSilta team have been putting into developing an improved cell culture medium for yeast.
Please take a look at this document (PDF) that describes the features of this new medium and how it can help you, if your research involves studying yeast:
BioSilta NEW EnBase technology now available for yeast biotransformations
05/08/11: Use IDT to Order 454 GS FLX System Extended MID Rapid Library Set
August 5, 2011 by Peter · Leave a Comment
This product came to my attention very recently, after talking to a customer. Access all available Molecular Identifier (MID) tags available. MIDs will allow identifying tags to be placed on multiple libraries so that they may be multiplexed for sequencing.
If you are a researcher who is using the 454 GS FLX system, it is possible to get the entire MID library from IDT (120 MIDs) from IDT. For customers that need more MIDs than the twelve supplied by 454 in the GS FLX Titanium Rapid Library MID Adaptors Kit, this Extended List provides additional sequences that have been optimized for MID applications.
01/08/11: Agilent SureSelect reaches a new Milestone: 100 Publications since launch in 2009!
August 3, 2011 by Peter · Leave a Comment
100 publications is a great reference source for researchers still unsure which technology they should use (the choice has expanded rapidly in those 2 years since SureSelect was released).
If anyone wants to receive some selected publications on SureSelect, please contact me using the form on the Contact Page.
Here is an extract from the press release:
Agilent’s Next-Gen Sequencing Target Enrichment System Cited in 100 Scientific Publications in Just Two Years
SANTA CLARA, Calif., Aug. 1, 2011 – Agilent Technologies Inc.
(NYSE: A) today announced that its SureSelect Target Enrichment System for next-generation sequencing has reached a significant milestone by playing a key role in 100 published studies since its introduction in early 2009.
The 100th article is posted in Nature Genetics online (July 2011), by Simon J. Girard et al., Centre of Excellence in Neuromics of Universite de Montreal. The investigators used SureSelect All Exon kits to enable them to identify mutations by analyzing schizophrenia sufferers and their unaffected parents. “A work of this scale would not have been possible before the era of high-throughput sequencing and exome capture,” Girard said. “Using the SureSelect kit, we were able to capture the exomes of 14 schizophrenia subjects and identify 15 de novo mutations. These mutations could be the hallmarks of a new era for the field of schizophrenia genetics.”
“The very rapid adoption of SureSelect by the genomics community is gratifying,” said Emily Leproust, Ph.D., Agilent director, Applications and Chemistry R&D. “We launched the first commercial in-solution target enrichment product just two years ago, and SureSelect’s performance and flexibility has led to it being the most commonly cited target enrichment tool on the market. It’s very exciting to see how researchers use SureSelect to overcome formidable challenges.”
SureSelect target enrichment has enabled researchers to identify mutations associated with more than 50 Mendelian diseases, 10 different types of cancer, and other complex diseases such as schizophrenia and Parkinson’s. The breakthrough findings of these studies published in high-impact journals demonstrate the research significance of targeted resequencing using SureSelect to enable the identification of variants associated with different diseases.
The SureSelect platform offers the most complete offering of catalog and custom capture kits, including comprehensive exome kits for human, mouse, and other model organisms, and flexible custom DNA or RNA target enrichment solutions, on all major next-generation sequencing platforms. In addition, Agilent offers library quantification qPCR kits and its Bioanalyzer line for next-generation sequencing library quality control. Agilent’s Bravo Liquid Handling System automates the next-generation sequencing workflow.
