11/04/14: HaloPlex Publication List

April 11, 2014 by · Leave a Comment 

HaloPlex Banner

A collection of publications that used HaloPlex Target enrichment in Cancer Research and Inherited Disease Research.

Click Here or on the picture above to download a PDF with the HaloPlex Publication List.

10/04/14: Time-Limited Offer on the 2200 TapeStation for Bioanalyzer Owners

April 10, 2014 by · Leave a Comment 

Upgrade to a TapeStation

Are you the owner of an Agilent 2100 Bioanalyzer instrument and based in Denmark? If yes, then you might be interested in a special offer on Agilent’s 2200 TapeStation. There is a great discount on the TapeStation if you already own a Bioanalyzer. Just contact me for details, using the form below and I’ll be happy to let you know what it is.

Note: this offer ends April 30th 2014 – so be quick!

 

09/04/13: Easing the Transition to Automated NGS Sample Preparation

April 9, 2014 by · Leave a Comment 

 NGS Automation Set Up

A nice article on transitioning from manual NGS sample prep. to using automation, from Genetic Engineering and Biotechnology News

28/03/14: News About The WIN Symposium, Paris, June 23-24

March 28, 2014 by · Leave a Comment 

140328 Agilent WIN Symposium

I’m posting this on behalf of Agilent. The WIN Symposium has a good reputation.

Agilent, being a proud founding member of the WIN consortium for personalized medicine, invites you to the WIN 2014 Symposium, in Paris, from June 23rd to 24th.

WIN Symposia are an initiative of the WIN Consortium, a non-profit global collaboration of academic, industry, health plan, and patient advocacy organizations dedicated to bringing the most promising advances in precision cancer medicine to patients worldwide.

Mr. Serota, President and CEO of Blue Cross and Blue Shield Association, joining other prestigious leaders, will present keynote lectures during the Symposium, including:

 

Robert Weinberg, Cambridge, MA (USA) Leroy Hood, Seattle (USA)
René Bernards, Amsterdam (NL) Guido Kroemer, Villejuif (France)
Hans Clevers, Utrecht (Netherlands) Bob Löwenberg, Rotterdam (Netherlands)

 See below some important links:

 

Program
Discover the detailed WIN 2014 program with all lecture titles and speakers names here.
Call to abstracts!
View abstract submission and abstract preparation guidelines here.
Linkedin
Join WIN Linkedin group to be informed about the Symposium, discover like-minded professionals and join discussions here.
Registration
Don’t miss this unique opportunity to interact directly with the world’s leaders in innovations in cancer patient management. Register now here.

 

24/03/14: Same Day, Cost-Effective Aneuploidy Detection with Agilent Oligonucleotide array CGH and MDA Single Cell Amplification Method

March 24, 2014 by · Leave a Comment 

Human egg cell isolated on white background

An interesting and potentially useful application coming from Agilent: the ability to analyze single cells for aneuploidy, using microarray-based comparative genomic hybridization (aCGH). There are several applications where this ability could be useful, for example pre-implantation (IVF), cancer and noninvasive prenatal testing.

Agilent have recently hosted a webinar, given by Ali Hellani, Founder, Viafet Genomic Center, Dubai. This webinar is now available to download and view for free (you need to fill in a few details at registration).

Access the webinar here

The abstract for the talk is as follows: The ability to characterize individual genomes in single cells is very important in pre-implantation genetics research in order to find the best protocol for diagnostic applications. While traditional FISH and PCR based techniques have been used for this purpose, their application has been narrowed by the limited number of loci that can be analyzed simultaneously. Recently, BAC arrays containing a few thousand probes have been used, delivering low-resolution results. Agilent’s high- resolution CGH microarrays with an optimized protocol would be well suited for the detection of aneuploidies in single cells.

In light of the time sensitive nature of pre-implantation genetics research and the need for an economical method to screen many samples in a high throughput environment, Dr. Hellani developed a same-day, cost effective protocol using the Agilent SurePrint G3 Human CGH 8x60K or 4x180K Microarrays and a Multiple Displacement amplification (MDA) method. The total time from amplification to data analysis can be as short as 6.5 hours. Dr. Hellani’s method allows for the processing of more samples per slide and the generation of high molecular weight DNA suitable for CGH and other applications, such as next generation sequencing. Utilizing this short, cost-effective protocol, copy number changes in individual genomes amplified from single cells can be accurately identified.

 

Access the webinar here

19/03/14: Resources for Researchers in Cancer

March 19, 2014 by · Leave a Comment 

Cancer word cloudI have put together a package of different research tools that are available to researchers in the cancer field. In the past, this would have involved talking to interested researchers and then sending an email with a whole bunch of attachments. Now, in “the interest of saving your mailbox,” I have assembled a number of useful documents in one place (nothing special, just a folder in my DropBox account). If you are interested to get access to this information, please fill in the contact form below.

Subjects covered include:

If any of this sounds interesting to you, please fill in this contact form and let me know:

Comments or questions are welcome.

* indicates required field

 

13/03/14: Accelerating NGS Research Through Automation

March 13, 2014 by · 1 Comment 

welcomeImage

My own experience has seen the difference that automation can make to throughput in next generation sequencing laboratories. For example, I’ve been told by one customer who set up an Agilent NGS Automation system in their laboratory, that it originally took two technicians three months to process 200 samples manually. After installation of an Agilent Bravo, they increased their throughput to 500 samples per week.

Agilent are currently running a campaign on automation, with resources, videos etc. that any researchers interested in this subject will find useful.

Access NGS Automation Resources

 

06/03/14: Agilent Compliance Tour – Copenhagen May 2014

March 6, 2014 by · Leave a Comment 

It seems that more and more labs are having to get some kind of certification. From what I can tell from talking to those of my customers who get GLP/GMP, it involves a lot of hard work and stress to put this in place. So, for those in Denmark who have already gone through the pain, or are thinking about it, Agilent’s upcoming Compliance Tour, stopping off in Copenhagen might be of interest.

Check out the Agenda and Register

 

Attendance is Free

 

28/02/14: Upcoming Webinar – Utility of an Automated SureSelect NGS Panel for Understanding Disorders Featuring Aortopathy

February 28, 2014 by · 1 Comment 

researcher Watching an online eSeminar

Agilent, together with GenomeWeb, are organising a webinar that encompasses targeted sequencing by NGS and automation of the next-gen sequencing workflow. The webinar will occur Tuesday March 25th 2014.

In this online seminar, Dr. Whitney Wooderchak-Donahue of the University of Utah and ARUP Laboratories shares the findings from sequencing 200 samples using an aortopathy sequencing panel developed at ARUP laboratories.Aortopathy is a group of disorders that includes aneurysms, dilation, and tortuosity of the aorta. Although the FBN1 gene plays a major role in pathogenesis, several other genes are known to be involved. Because of the phenotypic overlap and genetic heterogeneity of these disorders, ARUP developed a next generation sequencing panel to detect mutations in seventeen genes that cause thoracic aortic aneurysms.Dr. Wooderchak-Donahue and colleagues used a Bravo automated liquid handling instrument and custom SureSelect capture enrichment probes from Agilent Technologies to target the seventeen genes associated with aortopathies. NGS results were analyzed using an internally developed program, and mutations were confirmed using Sanger sequencing.

This webinar will detail how the aortopathy NGS research panel enables the identification of mutations in genes from individuals with disorders featuring aortopathy, including Marfan and Marfan-like syndromes.

 

You can register for the webinar here

A Q&A session will follow Dr. Wooderchak-Donahue’s presentation.Speaker:Whitney Wooderchak-Donahue
Adjunct Assistant Professor, Department of Pathology, University of Utah; research and development scientist, ARUP Laboratories

14/02/14: Release of Agilent SureCall v2.0 – Now with SureSelect Support

February 14, 2014 by · Leave a Comment 

1402 SureCall Figure

This is a good development in the story of Agilent’s free data analysis software, SureCall. Users of both HaloPlex and SureSelect will now be able to use the software, which is improving in quality all the time.

Highlights of New Features

  • SureSelect support
  • Exome analysis: HaloPlex and SureSelect
  • Find copy number changes with an in-house developed algorithm
  • Quickly identify somatic mutations in tumor versus normal sample analysis and de novo mutations with trio analysis

The Minimum You Need to Know About SureCall

  • SureCall is a sequencer-to-results solution which will increase throughput without increasing costs or requiring extensive bioinformatics resources
  • SureCall provides an end-to-end data analysis solution – from alignment to categorization of mutations
  • SureCall is part of Agilent’s market leading NGS Target Enrichment solution for clinical research
  • SureCall is available free-of-charge from Agilent’s website: www.agilent.com/genomics/surecall (available for PC 12Feb; Mac version available April)

10/02/14: Agricultural Biotechnology Symposium, Amsterdam 25-26th February

February 10, 2014 by · Leave a Comment 

Animal and Plant Symposium

Agricultural Biotechnology, which I guess means the application of biotechnology to agriculture, is of great interest because it is where research starts to be applied in ways that affect the food we eat, the energy we use and how we “do” agriculture. You Do Bio has quite a lot of customers who are working in this field – a couple of weeks ago I was at the Plant Biotech Denmark meeting as an exhibitor. With the general widening of the use of genomics research tools in research, it makes sense Agilent is planning their first European Animal and Plant Symposium which will be hosted in Amsterdam, February 25th and 26th 2014.

This Symposium will be over two days attracting leading scientists within the Agricultural Biology field, working in gene regulation, epigenetics, copy number/mutation detection and molecular biology using next-generation sequencing, microarrays and RT-qPCR/PCR. I think Agilent has done a great job in attracting some interesting outside speakers for this symposium. I know from experience how hard it is to get this number of speakers organized and available on those particular days of the meeting.

The meeting is open to all who work within the areas of:

  Food   Parasitology
  Plants   Veterinary
  Microbiology   Animal Genomics Research

Another focus is to investigate how such technologies and applications assist to address key concerns of the scientific community and to overcome current challenges in Agriculture Genomics Research.

  Discover the most up-to-date agenda here.

To register for the meeting please submit your details here.

Participation is free of charge but seats are limited!

I lived in The Netherlands for 4½ years and really like Amsterdam. It is also a fairly inexpensive place to fly to and stay. I wish I was going myself!

11/11/13: Designing Custom Oligo FISH Probes for the Detection of Chromosomal Rearrangements in FFPE Tissues

November 13, 2013 by · Leave a Comment 

 SureFISH in FFPE Tissue

Agilent presented some interesting new technology developments at the ASHG meeting held in Boston last month. Various R&D groups at Agilent also presented some of their technology-related work in the poster sessions. These posters are available (for now) on Agilent’s website.

The subject of FFPE always seems to be of interest, particularly for scientists who can get access to these samples and mine them for information.

Click here or on the picture, right, to see the poster “Designing Custom Oligo FISH Probes for the Detection of Chromosomal Rearrangements in FFPE Tissues”

8/11/13: Detection of Rare Variants in Degraded FFPE Samples Using HaloPlex PCR

November 11, 2013 by · Leave a Comment 

HaloPlex FFPE Poster ASHG 2013Agilent presented some interesting new technology developments at the ASHG meeting held in Boston last month. Various R&D groups at Agilent also presented some of their technology-related work in the poster sessions. These posters are available (for now) on Agilent’s website.

Since FFPE seems to be a topic of interest to researchers in the NGS field (not long ago I attended a meeting in Aarhus dedicated to this subject), I reckon this could be of fairly widespread interest.

Click here or on the picture, right, to see the poster “Detection of Rare Variants in Degraded FFPE Samples Using HaloPlex PCR”

16/10/13: A Webinar – Eliminating Bottlenecks and Managing Quantity and Quality in Genomics Research

October 16, 2013 by · Leave a Comment 

131016 Webinar

This should be interesting if you are considering automating any part of your genomics research. Based on reading the description, it should be an honest appraisal of approaching the issue of automating processes that is not afraid of addressing the difficulties that users will always encounter.

  • Broadcast Date: Wednesday, October 30, 2013
  • Time: 11 am ET, 8 am PT

The times are not super-convenient for Europeans, but usually these things are available as a recording later and if you register, you get access to the recording.

The seminar is organised by Genetic Engineering News (GEN). You can learn more about it and register here.

16/10/13: Two Important Updates to Agilent’s SureSelect Product Lines

October 16, 2013 by · Leave a Comment 

131016 SureSelect Manual Update

Agilent have recently announced two important and interesting announcements regarding their SureSelect product line:

1. Updated SureSelect Manual Low Input Protocol:

Agilent have developed a protocol that supports lower DNA input utilizing our current XT/XT2 kits and updated the existing manuals with an additional low input chapter.  Here are some highlights to remember: 

  • The standard input chapter still supports 3µg and 1µg for SureSelect XT/XT2 respectively, while the low input chapter supports 200ng/100ng for SureSelect XT/XT2 respectively.
  • The low input protocol was developed utilizing Agilent’s current  SureSelect XT/XT2 kits and requires no kit changes.  This means that current XT/XT2 kits remain the same and they continue to be compatible with all existing baits. 
  • A low input automation protocol will be available by the end of the year. 
  • In the following links, you can download the updated SureSelect XT and SureSelect XT2 manuals

2. SureSelect for Ion Proton is Now Available

The highly anticipated SureSelect for Ion Proton is Now Available for Quotes and Orders.  Here are some highlights: 

  • SureSelect TE Reagent Kit for Ion Proton is compatible with all current SureSelect XT baits.  Custom designs continue to be supported by SureDesign and Agilent’s Design Service Team.
  • The protocol uses Life Technologies library prep kit, which is a Covaris optional, enzymatic shearing library prep.

Agilent have succeeded in continuing to provide high sensitivity, specificity and coverage with greater than 99% SNP concordance rate in their Ion Proton protocol.

Anyone interested in learning more, please contact me directly.

16/10/13: An Important Announcement Regarding eArray

October 16, 2013 by · Leave a Comment 

eArray Announcement SureDesign

The following message has come from Agilent concerning their eArray online software. If you’re registered with e-Array, you will probably have received this already, so this post might be useful if you end up deleting that mail…

WHAT’S HAPPENING?

On November 18th Agilent is transitioning CGH, ChIP-on-chip, and DNA Methylation custom design work spaces from eArray to SureDesign.

Why are we transitioning CGH, ChIP-on-chip, and DNA Methylation to SureDesign?

  • Speed: Query and retrieve probe designs up to 5X faster than eArray. Design in minutes.
  • Accessibility: a more intuitive, redesigned user interface means a smoother work flow from start to finish.
  • Flexibility: enjoy the same unique flexibility in the creation of custom microarray designs and oligo libraries. Target specific chromosomal regions of interest, and select orders of no minimum size.

WHO IS IMPACTED?

  • Anyone who is an active eArray user.

HOW ARE YOU IMPACTED?

  • CGH, ChIP-on-chip, and DNA Methylation array design spaces will transition from eArray to SureDesign. To access custom designs and workspaces, account holders will log in through SureDesign.
  • CGH and ChIP-on-chip design spaces will be retired from eArray and all user data will be migrated to SureDesign.

eArray users will continue to have access to Expression, SureSelect Capture, SureSelect RNA enrichment, and microRNA design spaces.

13/09/13: eSeminar – Flexible Gene Regulation Solutions for Bacterial, Plant and Animal Sciences (Agricultural Biotech.)

September 13, 2013 by · Leave a Comment 

Cow_Agricultural_Biotechnology

Agilent are hosting a free online “eSeminar” for scientists involved in the Agricultural Biotechnology field. This will be held on Wednesday September 25th, 2013 at 1630 Central European Time (CET).

The abstract from the eSeminar reads as follows: “Today`s agricultural biologists have access to a variety of technologies at their disposal for studying genetic information. Such technologies include next-generation sequencing, microarrays, RT-qPCR/PCR and mutagenesis. By providing a complete portfolio of integrated gene regulation workflow solutions, Agilent gives you the power and tools needed to progress your science in plant, bacteria and animal genomics.

We have fully customizable content for maximum flexibility in experimental design utilizing catalog to custom microarrays and our market leading SureSelect products for non-human and model organisms.

From reproductive to crop science, Agilent has the scientific agility to shorten your time to market with customizable solutions for Agricultural Biotechnology.”

You can learn more and Register here.

09/09/13: This is really good – Agilent’s Courses About the Basics of NGS

September 9, 2013 by · Leave a Comment 

NGS Back to the Basics Agilent

Agilent have come up with a really excellent idea. They will be running a series of  ”NGS 101″ eSeminars for researchers to learn the basics of NGS. While Agilent do not supply any kind of next generation sequencing platform, they do have tons of knowledge from developing their market-leading SureSelect and HaloPlex target enrichment kits. I expect these course to be extremely useful to a wide range of interested scientitsts.

The NGS 101 courses run from 8-11 October.

Click here to Register

05/08/13: Online Videos Demonstrations for Agilent’s Genomics Products!

August 5, 2013 by · Leave a Comment 

Online Learning Genomics

This is great. A whole new set of videos (I think I counted seventeen) demonstrating the use of Agilent’s genomics products. The following categories are available:

  • HaloPlex Hands-On
  • SurePrint Microarrays Hands-On
  • SureSelect Hands-On

Hands-On Demonstrations of Agilent Genomics Products

27/06/13: For Protein Enthusiasts – Agilent’s OFF Gel Fractionator for Proteins and Peptides

June 27, 2013 by · Leave a Comment 

OFF Gel Fractionator Pic

Although You Do Bio is primarily a site that benefits genomics products and researchers, I do occasional forays into the protein / proteomics world, most notably with BioSilta’s product lines. Of course, the Agilent Bioanalyzer also does protein analysis too. However, Agilent also do a great, but little known instrument called the Off GEL Fractionator. The name does not give away what the product does (as is quite usual), but for anyone dealing with complex protein mixes, this great little device helps to fractionate the protein mix based on isoelectric point (pI).

The “OFF Gel” bit comes in, because the fractionation is done entirely in the liquid phase (as opposed to IN Gel), allowing samples to be drawn off easily for further analysis.

For anyone interested to learn more, take a look at this nice technical specification paper on the OFF Gel Fractionator.

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