31/05/10: Agilent microRNA Arrays updated to miRBase 15.0
May 31, 2010 by Peter · Leave a Comment
Just a quick update to researchers using, or interested in microRNA profiling. The excellent microarrays provided by Agilent have had their content recently updated to reflect the latest changes to miRBase, resulting in miRBase V.15.0.
Don’t forget that this content is entirely customizable to Agilent’s 8x15K microarrays via E-Array. You can learn more about the Agilent microarrays at this link.
Any questions? Please don’t hesitate to contact me.
31/05/10: Brilliant III performance on Applied Biosystems 7500 Fast and 7900HT qPCR systems
May 31, 2010 by Peter · Leave a Comment
Agilent’s new Brilliant III Ultra-Fast qPCR reagents sound and look really interesting for any qPCR users wanting higher throughput or fast results. Here are links to two PDF files that show data on the Applied Biosystems 7500 Fast and 7900HT qPCR systems:
Brilliant III 7500 Fast Data Sheet
Brilliant III 7900 HT Data Sheet
If you have any questions relating to Brilliant III, please contact me.
31/05/10: GEN Webinar on Applying Automation to NGS – available for download
May 31, 2010 by Peter · Leave a Comment
Solutions for Applying Automation to Next Generation Sequencing Sample Prep.
The original event was broadcast on:
Date: Tuesday, May 25, 2010
Time: 1:00 PM EDT
Duration: 75-minutes
http://event.on24.com/r.htm?e=210380&s=1&k=C2936186DABCC1615555937C04277D05
You can view the event archive at the link provided above.
You might want to download the PDF of the slides (available on the webinar page), because I found that the progression of the slide changes was sometimes behind the audio.
If you have any questions about automating your NGS protocols, or any other interest in automation, please contact me.
21/05/10: Applying Automation to NGS Sequencing Sample Prep
May 21, 2010 by Peter · Leave a Comment
Notification of an upcoming webinar hosted by Genetic Engineering News (GEN):
Solutions for Applying Automation to Next-Generation Sequencing Sample Prep.
Presenters: Broad Institute of MIT and Harvard, HudsonAlpha Institute for Biotechnology and Agilent Technologies.
Date: Tuesday, May 25th, 2010, 1300 EDT (1900 CET)
Be sure to register online through GEN at: http://www.genengnews.com/ngs
19/05/10: SurePrint G3 Arrays are now available for Gene Expression
May 20, 2010 by Peter · Leave a Comment
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.
19/05/10: BGI expands into Denmark
May 20, 2010 by Peter · Leave a Comment
BGI will create a $10 million European headquarters in Copenhagen, where it plans to eventually hire up to 150 scientists and support employees.
BGI will recruit between 20 and 50 people during the first year of the Copenhagen HQ — to be called BGI Europe — then establish a sequencing platform allowing for the hiring of between 50 and 100 people. The project will be China’s largest investment in Denmark.
Read the news in Danish here: http://www.dr.dk/Nyheder/Penge/2010/05/17/152105.htm
17/05/10: New NGS qPCR library quant kit
May 17, 2010 by Peter · Leave a Comment
This is a brand new product from Agilent that looks great. Designed to complement SureSelect sequence capture technology, it can also be used by any researcher who is working with next generation sequencing. In short, it is a fast and sensitive way to quantitate the amount of DNA in the library. The kit contains a DNA standard to which the library samples are compared.
Since the Agilent website is still being updated, you can get early access to the protocol here (PDF file): NGS Library Quant Kit
12/05/10: Custom Gene Synthesis
May 12, 2010 by Peter · Leave a Comment
Download the latest flyer from IDT (Integrated DNA Technologies) describing their gene synthesis services, available here.
There are special offers available to researchers who want to try out IDT’s gene synthesis services. Please contact me for more information.
10/05/10: Multiplexed sequencing with SureSelect – protocols available
May 10, 2010 by Peter · Leave a Comment
For researchers who are interested in the SureSelect target enrichment, the protocols are now available online at the link here. The publication numbers are G3360-90020 and G3360-90021, depending on whether you are using Illumina or SOLiD respectively.
07/05/10: “Capture Technique” enables researchers to study 49,000 year old DNA to study how similar and different neanderthals were to us
May 10, 2010 by Peter · Leave a Comment
Press release from Agilent:
Researchers from the Max Planck Institute (MPI), Cold Spring Harbor Laboratory (CSHL), Agilent Technologies Inc. (NYSE:A), and other prestigious institutions worldwide have shown that DNA capture techniques can greatly enable the sequencing of ancient Neandertal DNA, providing new insight into the nature of these prehistoric hominids.
The method, published in the May 7, 2010 issue of the journal Science, uses two rounds of “target enrichment” procedure to enrich ancient DNA from rare and precious bone samples so it can be sequenced. The complete article, “Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture,” is available at http://www.sciencemag.org/special/neandertal/.
“There is great interest in the relationship of Neandertals to people,” said senior author Svante Paabo of MPI. “Questions like, ‘Did our ancestors interbreed with Neandertals?’ are of interest, but also how our genome differs from that of Neandertals. Since Neandertals are our closest relatives, when we compare ourselves to them we can identify features in our genome that set us apart from all other organisms on the planet.”
“We were able to enrich Neandertal protein-coding regions where differences occurred on the human evolutionary lineage up to 190,000-fold using Agilent DNA array capture technology,” said Hernan Burbano of the MPI, one of the lead authors. “Ninety-six percent of all targeted positions were uncovered to an average sequencing depth of fivefold.”
“Attaining good coverage of the Neandertal genome had been a problem due to DNA contamination from microbes over the years,” Paabo added. “Simply sequencing, without first enriching for the genome, often didn’t work, especially where the contamination levels were high.”
Early in 2008, collaborators Emily Hodges and Greg Hannon of the Howard Hughes Medical Institute at CSHL were able to demonstrate through mock experiments that this problem could be resolved using target enrichment. Armed with this insight, the team began working on applying the technique to the contamination problem with ancient DNA. “Array hybridization capture technology” was originally reported by the CSHL group and is the subject of a longstanding collaboration with Agilent. The team recognized this as a promising method for recovering large regions of targeted sequence from Neandertal samples. “The method can also be used more widely with many other kinds of human remains,” Paabo observed.
“Working with ancient, sample-derived DNA is tough when compared with fresh samples,” said co-author Andy Bhattacharjee of Agilent’s Life Sciences Group. “Thirty to forty thousand years have passed since Neandertals walked on earth, and all that is left are ancient bones containing severely degraded DNA. The DNA itself has also undergone a sort of chemical aging (deamination).
“However, the worst offender is microbial contamination caused by colonization of microbes,” Bhattacharjee continued. “Therefore, removal of this contaminant DNA is of paramount importance, as this allows more coverage of the endogenous genome and therefore allows one to better decipher the genetic code. The capture methodology solves this big problem by enriching for Neandertal sequences and depleting contaminant DNA. It’s an elegant solution.”
“The methodology developed during this study can also be applied to other challenging studies in paleontology and archeology as well as in human forensics, which have been difficult to study systematically so far,” said co-author Leo Brizuela, also of Agilent. “This has been a very exciting and challenging project, and we appreciate the opportunity to work with this group.”
“These experiments were enabled by the flexibility and quality of the Agilent microarray platform on which the array capture technology is based,” Brizuela added. “In addition, we benefited from our experience in human exome sequencing, developed from our interaction with the Hannon lab at CSHL and Jay Shendure of the University of Washington.”
