For researchers interested in miRNA research, the Agilent microarrays are an excellent product for looking at expression of miRNAs across samples. Below is a link to an article describing how the high quality and consistency of Agilent’s microarray production pays off, when comparing data from arrays that represent different updates of the miRBase microRNA database.
The ESHG is one of the highlights of the conference season in Europe and is usually an incredibly popular meeting for researchers from Denmark and Sweden. So it should be again this year, with the conference being held in the German city of Nuremburg.
Two of the companies that are represented by You Do Bio will be holding their own satellite meetings at ESHG and both look good value:
1. Integrated DNA Technologies are holding the following satellite meeting:
Saturday, June 23, 11.45 – 13.15 hrs, Room Budapest
Oligonucleotides for Clinical and Research Applications – Why Quality Matters
2. Agilent Technologies will be holding the following event:
Monday, June 25, 11.40 – 13.10 hrs, Room Istanbul
Revolutionizing Human Genetics Research with new target enrichment system and high-resolution Oligo FISH technologies
This looks really interesting:
Please mark your calendar for Wednesday, June 6th as Agilent Technologies and Moran N. Cabili from the Broad Institute will host a free live webinar on lincRNAs.
|Title||Finding the missing LinCs of the transcriptome: The human body map lincRNA catalog|
|Presenter||Moran N. Cabili|
|Institution||The Broad Institute|
|When||Wednesday, June 6, 2012|
|Time||5:00 pm CET|
|Q&A||Session to follow with Anne Bergstrom Lucas,
Senior Research Scientist at Agilent Technologies
Large intergenic non-coding RNAs (lincRNAs) are emerging as key regulators of diverse cellular processes. Determining the function of individual lincRNAs remains a challenge. Recent advances in RNA sequencing (RNA-Seq) and computational methods allow for an unprecedented analysis of such transcripts. In this work, we present an integrative approach to define a reference catalog of over 8,000 human lincRNAs. Our catalog unifies previously existing annotation sources with transcripts we assembled from RNA-Seq data collected from ~4 billion RNA-Seq reads across 24 tissues and cell types.
Agilent has announced that e-Array v.7.8 has gone live from 23 February 2012. There are several new features and improvements, which are summarized below. They sound like very nice improvements:
A New eArray Workspace – Mutagenesis!
The eArray Mutagenesis workspace enables custom design for the Agilent QuikChange Oligo Library Mutagenesis System, a novel method for generating a rationally designed library of mutants. This new system enables researchers to precisely target and mutate every codon in up to 20 regions of 50 amino acids or less. It is an easy and rapid method for mid-throughput mutagenesis that allows customers to complete single amino acid scanning, codon saturation, or combinatorial mutagenesis in a single day. Please note that the QuikChange Oligo Library Mutagenesis System is currently available only through an early customer access program.
Three New Catalog SureSelect Kits – Human All Exon v4, Human All Exon v4 plus UTRs, and Human Methyl-Seq
These new SureSelect Target Enrichment kits are now available in eArray, along with a new SureSelect part number schema.
A New Zebrafish Genome version (Zv9) for Custom SureSelect Libraries!
eArray 7.8 now offers the Zebrafish (Danio rerio) Genome version Zv9 for custom SureSelect Target Enrichment, enabling customers to design their libraries using the most current Zebrafish content.
The eArray Development Team has implemented multiple performance and feature enhancements to improve customer experience.
Performance Optimizations for:
- Faster Bait and Probe Uploads
- Faster Creation of Bait Groups and Probe Groups
- Faster Probe Group Downloads
- Faster Design File Generation – Less waiting for new annotation files during “File Write in Progress.”
Longer Maintenance of Bait Tiling Parameters and Fate File Information for SureSelect Bait Tiling Jobs
- The storage time for design parameters and fate files for SureSelect bait tiling jobs is now six months. This was increased from two weeks and makes it more convenient for researchers to preserve the design parameters for important bait groups.
Increased Maximum Number of Baits that can be Downloaded from SureSelect Bait Search Results
- The limit for the number of baits that can be downloaded from bait search results has been increased to 50,000. Previous versions of eArray limited the maximum number to 10,000 baits.
Improved Packaging of Annotation File Download Archives
- Annotation file downloads are now packaged in a single .zip file archive. There are no longer multiple .zip archives nested within the main .zip archive.
Support for Tab-Text file for GenBank Accession Upload to RNA Enrichment Bait Tiling Wizard
- Users are no longer required to create a .zip archive of their gene list in order to upload it to the bait tiling wizard.
Updated Help and Info Links in the User Interface
- Embedded Help materials in the user interface have been thoroughly reviewed and updated.
This should be of interest to all of you who are using an Agilent scanner to scan your microarrays.
Agilent are pleased to announce the launch of the new standalone Feature Extraction version 11. Feature Extraction 11 represents an evolution in Agilent’s standalone software capability and is able to extract data from all Agilent’s microarrays, including CGH+SNP arrays.
Along with Feature Extraction 11 there is the introduction of the new QC Chart Tool v2.0, which is now integrated to Feature Extraction and installed with it.
In addition, the Feature Extraction product page has been updated to include the link to download the new FE 11.
Releasing the v18 probes in eArray allows researchers to design a miRNA microarray containing content specific for their experimental needs. In eArray, it is possible to create a custom miRNA design using probes to target any miRNA for any species included in miRBase.
The excellent quality of Agilent’s miRNA arrays, plus the ability to run 6 samples per microarray slide, makes them an excellent choice for miRNA researchers.
I have just heard that Agilent is organising a Genomics User Meeting to be held at the Wellcome Trust Conference Centre at the Sanger Genome Campus on 1st and 2nd March 2012.
The two days will cover researchers’ entire genomics workflow for microarrays and next generation sequencing and Agilent will be announcing some new product launches during the meeting. Good reasons to go!
The meeting is FREE to attend and will include all meals and refreshments, including a 3 course dinner on the Thursday evening. However you should arrange your own travel and accommodation.
There are a number of hotels available nearby including the Holiday Inn Express in Whittlesford http://www.hiexpresscambridgeduxford.co.uk/ and the Red Lion in Hinxton http://www.redlionhinxton.co.uk/.
Rooms are also available on site at a rate of £88.50 per night including breakfast. To book please call the conference reception on 01223 495000.
Please book as soon as you can as there are only 50 rooms available. The venue provides complementary car parking for all delegates and free wifi in all rooms.
PLEASE NOTE: Places at the meeting are limited so Agilent will be accepting registrations on a first come first served basis. Thank you for your understanding.
Please reply to me through the contact page to register your interest in the meeting and state any special dietary requirements. Also please let me know if you would be interested in presenting your research using Agilent’s genomics solutions during the meeting, in the form of a talk or poster.
Link to Agilent’s registration page for these eSeminars is here.
Example subjects include CytoGenomics and Whole Exome Sequencing
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!
I am pleased to inform you (well, if you are a researcher in Denmark at least) of Agilent’s Summer promotion on genomics products. The promotion is valid from now(28 June 2011) until August 31st 2011. Headlines below, with a bit more detailed information beneath each heading
Update 12 July: Agilent have a Summer Promotion webpage now live.
Purchase the New SureCycle PCR Instrument Together with the Mx3005P qPCR Instrument and get 30% off the Bundle
This is possibly the best offer of the whole promotion. The SureCycler is the hottest new instrument from Agilent, very cool (connect to it from a mobile device) with great specs. The Mx3005P is a well-proven and robust qPCR instrument that won’t let you down.
Purchase the Bioanalyzer with Agilent SureCycler 8800 or with >5000€ of Bioreagents and get 30% off the Total Bundle
Hmm. On second thoughts, perhaps this the the best of the Summer Promos. It really depends on what you are after. Of course, Bioreagents can mean a lot of things: PCR enzymes/kits, nucleic acid sample prep and qPCR reagents would be the most obvious. The combination of the Bioanalyzer with qPCR reagents sounds like a good combination to me, given that the Bioanalyzer is great for doing QC on RNA.
Get 50% off Absolutely RNA extraction kit when you purchase Bioanalyzer reagents
For those of you who are reguarly ordering Bioanalyzer kits (and that means lots of you), this is a great opportunity to try out one of Agilent’s best nucleic acid purification lines. The Absolutely RNA extraction kits come in a number of size options (mini-, micro- and nano-prep) and there are kits for miRNA and FFPE samples too. This is really a great excuse for you to try out these kits, especially if you haven’t had a lot of success with what you are currently using.
10,000€ discount on your genomics consumables order when you purchase an Agilent Bravo Automated Liquid Handling Platform
OK, so not everyone has the money available for an Agilent Bravo. However, if you are in the market for a small-footprint, very fast and accurate pipetting workstation, you really have to consider the Bravo. You will save many many days of work by having a Bravo in your lab, not to mention saving your pipetting thumb!
10,000€ (about DKK 75K) will get you a lot of genomics consumables.
Genespring and exon arrays: buy 5000€ of exon arrays and get 25% off your Genespring annual license, buy 10k€ of exon arrays and get 50% off the annual license.
Yes, it is that simple. Purchase Agilent’s high-quality exon arrays and get a big saving on the GeneSpring license (which you can then use to analyse all that lovely data and put into a biological context).
So that is the summary of Agilent’s Summer Promotion on genomics products. It looks pretty good to me and will mean that you come back from your Summer holiday with new gear to get into your research again after the break.
This post is to alert genomics customers who have an Affymetrix system that Agilent are offering a trade-in deal that allows them to get 50% off the Agilent High-Resolution Scanner. Any arrays purchased at the same time will also receive the 50% promotional discount.
The promotion is valid from now until December 31st 2011. Further details are available on the Agilent website.
Agilent Technologies invites you to their Genomics Roadshow.
Come along and find out more about Agilent’s microarray & qPCR platforms and get the latest update on SureSelect - target enrichment for Next Generation Sequencing and GeneSpring 12 – analysis software for microarrays, MS and Next Generation Sequencing data.
The Dates and Locations for Denmark are:
Copenhagen – March 30, 12:30-17:00, DTU
Aarhus – March 31, 12:30-17:00, Aarhus University
· Microarray applications – Gene Expression, Exon, CGH+SNP, miRNA & Custom array
· Genespring – Data analysis in Multi Omics Research – Analyzing MS, microarray and NGS data.
· SureSelect – Target Enrichment for Next Generation Sequencing
· Automation in genomics
· Improved detection and quantification in Real-Time PCR
Agilent have started an eSeminar series (kept it kind of quiet, if you ask me) that covers some very interesting subjects. Upcoming events include eSeminars on SureSelect, exon arrays, gene expression, methylation. Seminars can be viewed live, or downloaded later.
The main eSeminar page is here.
Agilent have announced the release of Agilent Genomic Workbench 6.5, which includes analysis capabilities supporting the new SurePrint G3 CGH+SNP Arrays. This feature allows the CGH+SNP arrays to be used for simultaneous detection of copy number changes and copy neutral LOH/UPD in the same workflow.
Exciting new features in the AGW 6.5 release:
- Ability to analyze Agilent CGH+SNP microarray data to identify and visualize copy number and copy-neutral LOH calls side-by-side.
- Easy installation and on demand data download allows users to install fully functional AGW6.5 in less than 30 minutes.
- Agilent Literature search CytoScape plug-in allows user to design custom microarrays around biological context of interest through eArrayXD.
- Entire Agilent SNP data set is available for download and search for designing custom CGH+SNP microarray in eArrayXD.
- Genotypes of 5 HapMap reference samples are pre-loaded for usage in DNAAnalytics.
- More efficient QC reporting of Target Enrichment data in workflow mode.
This looks like a really exciting product release from Agilent.
Agilent’s CGH arrays are already an excellent product for cytogenetics customers. The possibilities of the platform have now been extended to include a set of Single Nucleotide Polymorphism (SNP) probes on the same microarray. Researchers can now obtain detection of copy number and copy-neutral variations simultaneously, such as loss of heterozygosity (LOH) and uniparental disomy (UPD) on a single array.
Current content source database includes over 28 million predesigned, in silico-validated human CGH probes that span exonic, intronic, intergenic,CNV, pseudoautosomal, and segmented duplication DNA regions, and SNP probes for ~65,000 SNPs.
I was talking to a researcher yesterday who is very interestedin the possibilities that this new product can offer to his research projects. If you too would like to learn some more, please contact You Do Bio.
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.
Q: What is the process for ordering a design through eArray ?
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.
The link below goes to a detailed video (47 minutes) on loading, hybridizing and washing Agilent microarrays. Extremely useful, whether you are just starting out, or if you are an experienced user, but just need to “brush up” on your skills:
Agilent are pleased to announce the launch of new SurePrint G3 Promoter Microarrays. As the G3 product portfolio continues to expand, Agilent have updated the content for catalog human and mouse products using the latest genomic databases. These microarrays will be available as 1x1M and 2x400K formats enabling four times the density and coverage capabilities as compared to the existing SurePrint HD formats. They will be available as kits of 5 slides each and as single slides.
For more information on these slides, please visit the product page on the Agilent website here.
Agilent has expanded its gene expression platform to take advantage of their new, higher density array formats. Human and mouse arrays are now available in 8 x 60K format, while custom arrays are available in unlimited options using the formats 8x60K, 4x180K, 2x400K, and 1x1M.
Agilents new genomics website has been updated to reflect the news. Click here to learn more, or on the picture below.
Agilent has developed their Gene Expression Workflow: Quick Guide. This guide outlines in detail the steps recommended for processing FFPE samples from RNA isolation through to hybridization to microarrays.
If you have any questions about this, please use the Contact Page.