25/08/10: Here at Epigenetics & Stem Cells Conference
August 25, 2010 by Peter · Leave a Comment
I am exhibiting at the Epigenetics/Stem Cell conference at the Biologisk Institut in Copenhagen until Friday lunch. Come along and say hello (and maybe learn something too).
Conference link is here.
25/08/10: Agilent release SureSelect Human All Exon v.2. Content developed in collaboration with Broad Institute
August 25, 2010 by Peter · Leave a Comment
SANTA CLARA, Calif., Aug. 24, 2010 — Agilent Technologies Inc. (NYSE: A) today introduced the SureSelect Human All Exon v2 Target Enrichment kit, which was developed in close collaboration with the Broad Institute of MIT and Harvard. The kit, the 15th SureSelect product in Agilent’s portfolio, is a single tube assay that allows researchers to streamline experiments by sequencing the expressed genome while discarding regions not of interest.
The SureSelect platform is well-proven for enabling genetic discovery, evidenced by recent key discoveries into Mendelian diseases and heritable cancer. This year alone, the SureSelect Target Enrichment System has been cited in eight papers covering research into a wide range of heritable disorders.
Agilent offers an industry-leading three All Exon designs, two developed with the Broad Institute and one developed with the Wellcome Trust Sanger Institute and Gencode. The original Agilent Human All Exon Target Enrichment kit was introduced in September 2009. The new 38 megabase (Mb) kit design adds content recently determined to be in the expressed genome. This content also is found in Agilent’s second product targeting the human exome, the SureSelect Human All Exon 50 Mb kit, developed in partnership with the Wellcome Trust Sanger Institute and Gencode.
“We are happy with the most recent outcome of our long-standing collaboration with Agilent,” said Stacey Gabriel, Ph.D., co-director of the Genome Sequencing Center at the Broad Institute. “At Broad, we are continually developing our protocols to improve performance and enable the most efficient discoveries in human genetics. This new product from Agilent is just one of several anticipated improvements we will make available with Agilent to geneticists.”
“The Broad Institute has been utilizing this updated version of the Human All Exon kit for several months, and it works very well in our production pipeline,” added Sheila Fisher, assistant director of Technology Development for the Genome Sequencing Center at the Broad Institute. “We have used this kit to successfully target and sequence the exomes of more than 5,100 human samples from a variety of cancer and heritable disease studies.”
“The Broad Institute worked with us to define the first version of the SureSelect Human All Exon kit,” said Emily M. LeProust, Ph.D., Agilent director of Genomics Application Development, “and has continued this relationship to further define and improve the performance of this already powerful capture technology. We believe that it will continue to be a highly useful research tool for discovery of mutations linked to heritable disease and cancer.”
The SureSelect Human All Exon v2 kit design covers:
- 99.01 percent of human exons defined by the NCBI Consensus CDS Database from September 2009;
- 93.29 percent of RefSeq genes;
- 95.07 percent of RefSeq transcripts from June 2010; and
- 90 percent of miRNA in miRBase v14.
The kit targets just over 38 Mb of the human genome in a single tube reaction. In addition to the new content, teams at the Broad Institute and Agilent have carefully re-balanced the mixture of probes to maximize capture efficiency and uniformity across the exome.
Agilent’s SureSelect Target Enrichment System offers the broadest range of target enrichment products and the most highly optimized protocols for a diverse set of sequencing methods and platforms. There are now 15 products in the SureSelect portfolio, with many more in development. SureSelect products are available for enrichment of target sizes ranging from smaller than 200 Kb to more than 50 Mb in a single tube. Protocols now support Illumina end sequencing, paired-end sequencing and indexing protocols in addition to fragment library format, paired-end sequencing and barcoding on the SOLiD System.
Users of Agilent’s eArray xD desktop design tool can improve the efficiency of their research by easily designing custom products to target any genome of interest, all in a single tube. Agilent also offers the eArray online design tool, enabling users to customize pre-defined SureSelect kits such as the SureSelect Human All Exon series of products.
For more information, visit www.agilent.com/genomics/sureselect. Find eArray at www.agilent.com/genomics/earray.
25/08/10: New! Order your Microarray Designs through e-Array
August 25, 2010 by Peter · Leave a Comment
A short announcement for users of e-Array. Ordering your custom designs has become a little bit easier. Find out how, here, or continue reading.
You can now send your custom or catalog microarray/ SureSelect orders directly from eArray, to your Agilent Genomics shopping cart to place an order.
FAQ
Q: What is the process for ordering a design through eArray ?
A:
1) Select ‘Order’ under actions for the microarray design you wish to place an order for.
2) Enter the number of slides you wish to order, and select ‘Next’.
3) Review your order and select ‘Add to Cart’
4) Select Checkout
Q: What if I do not have an online store account ?
A: You will need to be registered with the Agilent Genomics web site in order to be able to place orders through the online store. Once you login, a cookie is saved to your local machine, making the move from eArray to the Genomic Online Store seamless.
Q: I still cannot order via the online store, what is wrong?
A: You will need to make sure that you have enabled the “Place online ordering” option under My Account > Preferences. If you need assistance with the online store, please contact customer support.
17/08/10: What’s New from BioCision: Ice-Free PCR Sample Cooler
August 17, 2010 by Peter · Leave a Comment
Check out the latest cool product from BioCision! This looks rather good – a means to keep your samples cool for up to 10 hours on the bench, without the use of ice. Read the text below and follow the links to learn more.
Sample set up has never been easier or safer. Easy switch cartridges allow all day cooling—get up to 10 hours of ice-free cooling (0.5°C to 4°C) in a compact, portable system. No more contamination or mess from conventional ice methods. More >
No more re-charging time required. Unlike sealed plastic gel-filled cooling containers which require an extended overnight re-freezing interval, CoolBox performance can be extended indefinitely by simple cartridge switching. No down time, no hassle. More >
True iso-temperature during entire cooling period. The CoolRack thermo-conductive module inside the CoolBox provides unparallelled temperature control for all wells. Unlike gel-filled coolers, well-to-well variation will be < 0.1°C at all times. No more worry about uneven sample processing. More >
16/08/10: Article – Genomics At Agilent: Driving Value in DNA Sequencing
August 16, 2010 by Peter · Leave a Comment
Agilent CTO, Darlene Solomon, has co-written an article about innovation at Agilent Labs and how that plays a role in getting new products commercialized for researchers. Darlene collaborated with Emily Leproust and others, to write this great article related to Agilent’s strength in oligo synthesis, NGS workflow and synthetic biology.
You can access the article at the Agilent website here.
16/08/10: Agilent and IDT team up to offer complete and validated qPCR solution
August 16, 2010 by Peter · Leave a Comment
Agilent and Integrated DNA Technologies (IDT) are working together to provide researchers with new solutions for qPCR that offer:
- Greater flexibility
- Better qPCR efficiency
- Low Cq values
To learn more, take a look at the publication here. This shows data demonstrating the performance of the new Brilliant III qPCR mixes with IDT’s PrimeTime qPCR Assays.
16/08/10: New BioAnalyzer Publication on Protein Analysis
August 16, 2010 by Peter · Leave a Comment
Agilent has released a new BioAnalyzer publication concerning the use of the BioAnalyzer instrument for protein sizing and quantitation analysis. View a PDF file of this publication here.
ABSTRACT
The Agilent 2100 Bioanalyzer employs microfluidic capillary gel electrophoresis for protein analysis where fluorescence intensities of proteins are measured as a function of their migration times. Data analysis is performed by the Agilent 2100 Expert Software, automatically determining molecular weight and concentration of the proteins in the sample. This Technical Overview describes the underlying mathematical operations for obtaining protein size and concentration information.
16/08/10: New BioAnalyzer Publication on miRNA Analysis
August 16, 2010 by Peter · Leave a Comment
Agilent has released a new BioAnalyzer publication concerning the use of the BioAnalyzer instrument for miRNA quality analysis. View a PDF file of this publication here.
ABSTRACT
It is generally known that total RNA quality has a distinct influence on the validity and reliability of quantitative PCR results. In addition, the recently published MIQE guidelines focus on the pre-PCR steps and state the importance of RNA quality assessment. Various studies showed the impairing effect of ongoing RNA degradation on mRNA expression results. Therefore, the verification of RNA integrity prior to downstream applications like RT-qPCR and mircroarrays is indispensable. A fast and reliable assessment of RNA integrity can be done with the Eukaryote Total RNA Nano Assay of the Agilent 2100 Bioanalyzer. The importance of RNA quality should also be considered in new applications such as the investigation of miRNA expression profiles. With the Agilent Small RNA Assay, Agilent is offering one of the few possibilities for selectively estimating miRNA before expression analysis. However, by now little is known about factors affecting miRNA analysis. Herein, the important impact of total RNA quality on quantification of mRNA and miRNA should be considered.
04/08/10: Agilent Collaborates with Wellcome Trust Sanger Institute and Gencode to Develop Latest Human All Exon Target Enrichment Tool for Next-Gen Sequencing
August 4, 2010 by Peter · Leave a Comment
Agilent have just announced the release their new SureSelect Human All Exon design – the SureSelect Human All Exon 50Mb.
The new design is the most comprehensive exon capture kit available on the market. The new kit expands on Agilent’s current exon kit with additional validated content, developed by the Wellcome Trust Sanger Institute. Derived through deep RNA sequencing, the new design encompasses coding exons annotated by the GENCODE project as well as CCDS and RefSeq databases and incorporates exonic regions and non-coding RNAs to provide a capture size of approximately 50Mb.
The new kit comes with the quality, robustness and performance customers have come to expect from Agilent’s SureSelect products.
Highlights:
- Largest exon capture kit on the market – target approximately 50Mb with only 3ug input gDNA
- Designed with the Wellcome Trust Sanger Institute
- High capture specificity and coverage provides efficient sequencing and accurate SNP/variant calling
- Most complete representation of the exome available (99% of CCDS and 97% of RefSeq)
- The new kits should be available to order by Friday August 6th
Web Pages:
SureSelect Human All Exon 50Mb – Product Page – Overview
SureSelect Human All Exon 50Mb – Product Page – Details & Specifications
02/08/10: Agilent SureSelect for SOLiD Updates
August 2, 2010 by Peter · Leave a Comment
There are two important updates for everyone who works with the Agilent SureSelect Target Enrichment Platform on the AB SOLiD System.
Agilent SureSelect for Applied Biosystems SOLiD Updates:
1. Agilent SureSelect is fully compatible with SOLiD 4 paired-end sequencing:
The Applied Biosystems SOLiD 4 System supports paired-end and multiplexed paired-end sequencing. The current Agilent SureSelect Target Enrichment system is fully compatible with both of these SOLiD 4 paired-end workflows. Agilent SureSelect / AB SOLiD users should follow the current Agilent protocols for target enrichment, available at these links:
SureSelect Target Enrichment, Human All Exon, and Human All Exon Plus for AB SOLiD
SureSelect Target Enrichment for AB SOLiD Multiplexed Sequencing
…followed by the protocol in the Applied Biosystems SOLiD™4 System Templated Bead Preparation Guide.
2. The QPCR NGS Library Quantification Kit (AB SOLiD) G4881A:
The QPCR NGS Library Quantification kit (AB SOLiD) G4881A is available and is listed in the protocol for use with SureSelect kits for AB SOLiD Multiplexed Sequencing. Each QPCR NGS Library Quantification Kit provides reagents to quantify 84 libraries.
The QPCR NGS Library Quantification Kit product details, specifications, and manual are located on the QPCR NGS Library Quantification Kit product page.
02/08/10: Updated miRNA Arrays Available
August 2, 2010 by Peter · Leave a Comment
Agilent have recently launched updated human and mouse miRNA arrays for miRBase v14 content. The new v14 Rev2 designs were designed by Agilent R&D and have completed in house testing.
Additionally, new mouse and rat designs are available for miRBase v15.
All Agilent miRNA arrays allow the addition of customized content at no additional cost.
