BioMicroCenter:News

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(May 24, 2011)
(BioMicro Center News)
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=== JULY 2, 2011 ===
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Dear users,
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I hope everyone is having a great summer. I have a few updates for on recent changes in the BioMicro Center.
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First, by popular demand we are announcing that our RNA seq sample preparation service is officially accepting samples. This service requires 100ng of high quality eukaryotic RNA as input and is based on the Illumina TruSeq RNAseq kits coupled with the SPRIworks sample preparation robot. The initial price is $350/sample, which is a little more than then price of a microarray preparation. While the service is open, we are still in the tweaking stage and we are evaluating a number of different protocols that could reduce the total RNA amount or lower the quality of the RNA needed. We do hope to have these questions resolved in the very near future, but the quality of the data we have been getting has been sufficient that we wanted to open the service up to everyone.<BR><BR>
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Second, prices for all of our services were updated on July 1st. Many prices are decreasing. A few key things to notice:
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* Agilent microarray prices are dropping to be significantly lower than Affymentrix. A full experiment can cost $350/array.
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* HiSeq lane prices have decreased – particularly for paired end samples. GAII prices have also dropped a little.
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* Robotics usage prices are now set in two hour blocks instead of on a “per session” basis.
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* Fluidigm usage prices will be rising to help defray repair costs.
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The full list can be found '''[[BioMicroCenter:Pricing|on our pricing page]]<BR><BR>
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Finally, this month we have a number of personnel changes. Katie Sullivan and Justin Elliot will be returning to Northeastern with our thanks for six months of hard work, and our new co-ops Jessica Lebowitz and Kaitlyn Sanders, will be starting on July 5th. Jessica and Kaitlyn will be taking over operation of the BioAnalyzer/LabChip and other sample quality control services. In addition, we will be adding a new bioinformaticist, Dr. Huming Ding, to the Center in early July. Dr. Ding comes to us from the University of Toronto where he worked extensively with Dr. Charlie Boone on high throughput screening of genetic interactions and will be helping us establish pipelines for analyzing Illumina data. Please say hello and make them feel welcome the next time you stop by!<BR><BR>
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Best regards and have a happy Fourth of July!<BR>
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-Stuart Levine
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=== May 24, 2011 ===
=== May 24, 2011 ===

Revision as of 11:45, 2 July 2011

Image:BioMicroCenter-header6.jpg

Contents

BioMicro Center News

JULY 2, 2011

Dear users,

I hope everyone is having a great summer. I have a few updates for on recent changes in the BioMicro Center.

First, by popular demand we are announcing that our RNA seq sample preparation service is officially accepting samples. This service requires 100ng of high quality eukaryotic RNA as input and is based on the Illumina TruSeq RNAseq kits coupled with the SPRIworks sample preparation robot. The initial price is $350/sample, which is a little more than then price of a microarray preparation. While the service is open, we are still in the tweaking stage and we are evaluating a number of different protocols that could reduce the total RNA amount or lower the quality of the RNA needed. We do hope to have these questions resolved in the very near future, but the quality of the data we have been getting has been sufficient that we wanted to open the service up to everyone.

Second, prices for all of our services were updated on July 1st. Many prices are decreasing. A few key things to notice:

  • Agilent microarray prices are dropping to be significantly lower than Affymentrix. A full experiment can cost $350/array.
  • HiSeq lane prices have decreased – particularly for paired end samples. GAII prices have also dropped a little.
  • Robotics usage prices are now set in two hour blocks instead of on a “per session” basis.
  • Fluidigm usage prices will be rising to help defray repair costs.

The full list can be found on our pricing page

Finally, this month we have a number of personnel changes. Katie Sullivan and Justin Elliot will be returning to Northeastern with our thanks for six months of hard work, and our new co-ops Jessica Lebowitz and Kaitlyn Sanders, will be starting on July 5th. Jessica and Kaitlyn will be taking over operation of the BioAnalyzer/LabChip and other sample quality control services. In addition, we will be adding a new bioinformaticist, Dr. Huming Ding, to the Center in early July. Dr. Ding comes to us from the University of Toronto where he worked extensively with Dr. Charlie Boone on high throughput screening of genetic interactions and will be helping us establish pipelines for analyzing Illumina data. Please say hello and make them feel welcome the next time you stop by!

Best regards and have a happy Fourth of July!
-Stuart Levine


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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