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=== Nov 9, 2010 ===
=== May 24, 2011 ===
Dear users,<BR><BR>
We have a number of updates to let you all know about that have happened in the last few months. <BR><BR>
First, we have continued to expand our DNA sample preparation services. Over the past few months, we have been experimenting with the Nextera sample prep kit to complement our SPRIworks service. Where the SPRIworks system uses sonicated DNA, the Nextera kit is built to handle intact genomic DNA, using a transposase to fragment the DNA and is particularly suitable for applications that use entire genomic DNA, including copy number variation and de novo and resequencing projects. In addition, we have taken advantage of recent work from the Broad to improve our library representation by modifying our amplification protocol. The Nextera service is now available through BioMicro for the same price as the SPRIworks system and includes molecular barcoding of the library. For more information about the Nextera system, please email Ryan Sinapius.<BR><BR>
In the microarray area, we have made significant improvements to our Agilent microarray service. First, we have upgraded our scanner to 2um resolution, which will allow scanning of Agilent’s newest 1 million feature arrays. This has been coupled with an upgrade of the scanning and analysis software that can now handle additional quality controls.  In addition, we have been working with Agilent to bring down the prices of their microarrays and we will be able to offer them at a significant discount beginning in July that will bring the price of microarray analysis down significantly. For more information about changes in the Agilent platform, please talk with Manlin Luo.<BR><BR>
Finally, in response to user demand we have purchased a number of licenses for TIBCO Spotfire Analytics. Spotfire is a widely used data analysis and visualization tool. It can handle a number of clustering functions and statistical tests and has very robust graphical capabilities. If you are interested in trying out Spotfire, please contact Stephen Goldman.<BR><BR>
As a reminder, this email only goes out to people who are have used the BioMicro Center within the past couple years. Please feel free to forward this message on to anyone else who might be interested.<BR><BR>
Thank you all for your support,<BR><BR>
-Stuart Levine<BR><BR>
 
=== Jan 2011 ===
Dear Users,<BR><BR>
Dear Users,<BR><BR>
This month, though the generous contributions of Penny Chisholm and Chris Burge, we are pleased to announce the addition of an Illumina HiSeq2000 to our sequencing capacity. We have been testing the HiSeq for a couple months and have been able to obtain over 100,000 usable reads per lane. This service is now available to all CORE lab members. For those labs that do not require a full lane for each sample, we also can provide multiplexing of samples as part of our sample preparation service. More information about the HiSeq and multiplexing can be found on our website.<BR><BR>
I hope everyone had a great holiday. We have a couple updates as we begin the year.<BR><BR>
 
One of our goals for this year is to reduce our turnaround time as much as we can. We’ve taken a couple steps in this direction (though we have a long way to go!). First, we have brought a number of additional technicians on board. Michael Gravina joins us from Alnylam and will be working on the Illumina platform. Barbara Karampalas is joining us part time to work on automation. In addition we added two new coop students, Katie Sullivan and Justin Elliott, who will be taking Eris’ place as he returns to Northeastern, and we are looking to make an additional hire in the bioinformatics area (in collaboration with the Koch Institute Bioinformatics and Computing Core). Make sure you say hello the next time you stop by.<BR><BR>
The Technology Seminar Series is also continuing on. The seminar series is designed to showcase a different technology in the facility each week and to bring you up to date on the latest advances and future directions of the technology. The seminar is at noon in 68-180 on Mondays and lunch will be provided. We have asked the companies we have invited to bring their scientists to speak (not the sales team) so you have a chance to interact with them directly. The current list of speakers can be found [[BioMicroCenter:Technology_Seminar_Series|on our website]]<BR><BR>
In addition to new staff, we have also upgraded some of our equipment. This week we are adding a new Caliper LabChip system. The LabChip is a high throughput version of the Agilent BioAnalyzer (which uses Caliper technology) and can process hundreds of samples in a batch. Our on-site testing with the LabChip had a significant effect on the speed at which we were able to handle quality control. In order to automate the process, we will have to increase the minimum volume of sample we accept (to 5ul). For most applications, simply diluting your samples 2 fold prior to submission will be sufficient. We will be using the LabChip to handle high sensitivity DNA and standard RNA samples while small RNA, pico RNA and protein samples will continue to be run on the BioAnalyzer. Prices for the LabChip and the BioAnalyzer will be the same but we will be able to offer discounts on large sample submissions that are run on the Caliper. <BR><BR>
 
Finally, we are in the finishing stages of beta testing our new RNA-seq sample prep service.  An addition to our existing DNA sample prep, we will be able to accept submissions of total RNA for sequencing just as we do for microarrays. Our current protocol is derived from Chris Burge’s lab but we are also testing kits from NuGEN for digital gene expression (DGE) which we hope will offer microarray quality results for considerably lower costs. If you are interested in helping out and have samples you are willing to contribute, please contact Ryan Sinapius who is coordinating the effort. <BR><BR>
Finally, we have been able to negotiate a lower rate for the reagents for Illumina sample preparation. This price reduction went in to effect on Nov 1st and is listed on our website. We are always looking for ways we can reduce the cost of our services without compromising quality.  
As a reminder, this email only goes out to people who are have used the BioMicro Center within the past couple years. Please feel free to forward this message on to anyone else who might be interested.<BR><BR>
As a reminder, this email only goes out to people who are have used the BioMicro Center within the past couple years. Please feel free to forward this message on to anyone else who might be interested.<BR><BR>
Thank you all for your support,<BR><BR>
-Stuart Levine<BR><BR>


Thank you all for your support,<BR>


-Stuart Levine


=== Sep 12, 2010 ===
Dear Users,<BR><BR>
Today marks the beginning of our Technology Seminar Series. This seminar series is designed to showcase a different technology in the facility each week and to bring you up to date on the latest advances and future directions of the technology. This week’s speaker is from Nanostring which makes the nCounter, an imaging system that allows direct visualization of hybridization reactions. The seminar is at noon in 68-180 and lunch will be provided.  We have asked the companies we have invited to bring their scientists to speak (not the sales team) so you have a chance to interact with them directly. Following Nanostring will be Beckman-Coulter Genomics and then NuGEN. The current list of speakers can be found on [[BioMicroCenter:Technology_Seminar_Series|our website]]<BR><BR>
This past month, though the generous contributions of Chris Burge, Ernest Fraenkel and The Koch Institute we were able to add a new robot for Illumina sample preparation. The Beckman-Coulter SPRI-TE handles many of the routine steps in preparing Illumina libraries, including size selection. The SPRI-TE is available either as part of our DNA sample preparation services or as an a la carte service. You can learn more on our website and next week at the seminar.<BR><BR>
Finally, this month we will be saying goodbye to Allison Perrotta who has been a technician in the BioMicro Center for the past two years. Allison was instrumental in setting up our Illumina sequencers and has been involved in setting up our sample preparation service. We are currently conducting a search for her replacement (please send any good candidates our way) but we will miss her very much.<BR><BR>
Thank you all for your support,<BR>
-Stuart Levine


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Revision as of 12:01, 24 May 2011

HOME -- SEQUENCING -- LIBRARY PREP -- HIGH-THROUGHPUT -- COMPUTING -- OTHER TECHNOLOGY

BioMicro Center News

May 24, 2011

Dear users,

We have a number of updates to let you all know about that have happened in the last few months.

First, we have continued to expand our DNA sample preparation services. Over the past few months, we have been experimenting with the Nextera sample prep kit to complement our SPRIworks service. Where the SPRIworks system uses sonicated DNA, the Nextera kit is built to handle intact genomic DNA, using a transposase to fragment the DNA and is particularly suitable for applications that use entire genomic DNA, including copy number variation and de novo and resequencing projects. In addition, we have taken advantage of recent work from the Broad to improve our library representation by modifying our amplification protocol. The Nextera service is now available through BioMicro for the same price as the SPRIworks system and includes molecular barcoding of the library. For more information about the Nextera system, please email Ryan Sinapius.

In the microarray area, we have made significant improvements to our Agilent microarray service. First, we have upgraded our scanner to 2um resolution, which will allow scanning of Agilent’s newest 1 million feature arrays. This has been coupled with an upgrade of the scanning and analysis software that can now handle additional quality controls. In addition, we have been working with Agilent to bring down the prices of their microarrays and we will be able to offer them at a significant discount beginning in July that will bring the price of microarray analysis down significantly. For more information about changes in the Agilent platform, please talk with Manlin Luo.

Finally, in response to user demand we have purchased a number of licenses for TIBCO Spotfire Analytics. Spotfire is a widely used data analysis and visualization tool. It can handle a number of clustering functions and statistical tests and has very robust graphical capabilities. If you are interested in trying out Spotfire, please contact Stephen Goldman.

As a reminder, this email only goes out to people who are have used the BioMicro Center within the past couple years. Please feel free to forward this message on to anyone else who might be interested.

Thank you all for your support,

-Stuart Levine

Jan 2011

Dear Users,

I hope everyone had a great holiday. We have a couple updates as we begin the year.

One of our goals for this year is to reduce our turnaround time as much as we can. We’ve taken a couple steps in this direction (though we have a long way to go!). First, we have brought a number of additional technicians on board. Michael Gravina joins us from Alnylam and will be working on the Illumina platform. Barbara Karampalas is joining us part time to work on automation. In addition we added two new coop students, Katie Sullivan and Justin Elliott, who will be taking Eris’ place as he returns to Northeastern, and we are looking to make an additional hire in the bioinformatics area (in collaboration with the Koch Institute Bioinformatics and Computing Core). Make sure you say hello the next time you stop by.

In addition to new staff, we have also upgraded some of our equipment. This week we are adding a new Caliper LabChip system. The LabChip is a high throughput version of the Agilent BioAnalyzer (which uses Caliper technology) and can process hundreds of samples in a batch. Our on-site testing with the LabChip had a significant effect on the speed at which we were able to handle quality control. In order to automate the process, we will have to increase the minimum volume of sample we accept (to 5ul). For most applications, simply diluting your samples 2 fold prior to submission will be sufficient. We will be using the LabChip to handle high sensitivity DNA and standard RNA samples while small RNA, pico RNA and protein samples will continue to be run on the BioAnalyzer. Prices for the LabChip and the BioAnalyzer will be the same but we will be able to offer discounts on large sample submissions that are run on the Caliper.

Finally, we are in the finishing stages of beta testing our new RNA-seq sample prep service. An addition to our existing DNA sample prep, we will be able to accept submissions of total RNA for sequencing just as we do for microarrays. Our current protocol is derived from Chris Burge’s lab but we are also testing kits from NuGEN for digital gene expression (DGE) which we hope will offer microarray quality results for considerably lower costs. If you are interested in helping out and have samples you are willing to contribute, please contact Ryan Sinapius who is coordinating the effort.

As a reminder, this email only goes out to people who are have used the BioMicro Center within the past couple years. Please feel free to forward this message on to anyone else who might be interested.

Thank you all for your support,

-Stuart Levine

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