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== BioMicro Center News ==
 
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=== Nov 9, 2010 ===
 
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>
 
 
 
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>
 
 
 
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>
 
 
 
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
 
 
 
 
 
=== Aug 9, 2010 ===
 
Dear Users,<br>
 
There have been a number of significant changes in the BioMicro Center in the past few months and there will be more to come.  To keep you up to date, I will again be sending out a newsletter every month or two with highlights of what is going on. Unlike previous newsletters, these will only be sent to those who have used the facility within the past year or so, so be sure to spread the word if you see items that might be of interest to others in your lab!
 
====New equipment====
 
A number of pieces of new equipment have been added to the BioMicro Center, particularly in the area of high throughput screening. First, through an equipment grant sponsored by Wendy Gilbert, we have added a second robotic fluidics machine that is specifically geared for screening 96 and 384 well plates.  Unlike the older robot, this [[BioMicroCenter:Tecan_Freedom_Evo|Tecan]] has a plate manipulating arm that allows it to handle much larger experiments. We also have added the [[BioMicroCenter:RTPCR|Fluidigm Biomark]] which has been relocated from E17 and we are also in the evaluation phase for the [[BioMicroCenter:Nanostring|Nanostring nCounter]]. Both of these machines allow you to look at a large number of genes / SNPs across a large number of samples. The [[BioMicroCenter:RTPCR|Biomark]] is a nanofluidic RT-PCR machine that creates large matrices (either 48x48 or 96x96) of samples and primers, allowing you to do close to 10,000 RT-PCR reactions on a plate. The [[BioMicroCenter:Nanostring|nCounter]] uses a [[BioMicroCenter:Nanostring|“code set”]] of up to 800 genes to hybridize to dozens or hundreds of samples, then visualizes the single molecule interactions. The [[BioMicroCenter:Nanostring|nCounter]] is particularly interesting in that it does not require conversion of the sample to cDNA, or even purification of the RNA. Information about all of these instruments can be found on our website.
 
 
 
====New services====
 
We are happy to announce the beginning of sample preparation services for Illumina sequencing. We are introducing this service starting with double stranded DNA fragments (>100bp) such as de novo genomic sequencing, resequencing, ChIP-seq and RNA-seq that has been converted to cDNA. The service includes QC, end-repair, adaptor ligation, size selection and enrichment. Once samples are prepared, they are validated and added directly to the Illumina sequencing queue. Right now, this service is limited, but we are hoping to introduce multiplexing and RNA samples in the near future.
 
====Upcoming Events====
 
With so many changes both in new equipment and upgrades to current equipment we wanted to create an opportunity for you to learn more about the assays available in the facility. To help with this, we will be sponsoring a [[BioMicroCenter:Technology Seminar Series|“Technology Seminar Series”]] this fall. The weekly seminars will be at noon on Mondays (lunch will be provided). Each week we will showcase a different technology in the facility and bring you up to date on the latest advances and future directions of the technology. 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.
 
I hope you are having a great summer!<br>
 
-Stuart
 
  
=== May 13, 2010 ===
+
== JANUARY 9, 2013 ==
In order to increase the space available for equipment in the BioMicro Center, we are doing a little more remodeling. Please note the following changes:
+
Happy new years to everyone. A couple new things happening in BioMicro that we want to make everyone aware of. <BR><BR>
* The freezers have been relocated to the 304 hallway
+
First, this month begins a year long experiment in joining the BioMicro Center Informatics team and the KI Bioinformatics and Computing Core in to a single team. Our two teams have been collaborating for several years, sharing computational infrastructure, etc. but this year we will be formalizing and expanding the relationship with the goal of creating a more efficient unified core. Informatics analysis requests should still be sent to Charlie Whittaker or to myself as usual, but will be spread across the joint team based on expertise and on availability. You are also, as always, welcome to contact any of the informatics scientists directly. We hope this will allow us to reduce waiting times and to keep costs under control.  <BR><BR>
* The RT-PCR machines will be moving to the 316 entry.
+
During the trial period (and hopefully going forward), pricing for informatics will be available in two flavors. First, for projects needing routine work, the subsidized rate will be $70/h for all CORE members (Biology, BE, KI, CEHS). For more involved projects, we have second option to purchase a “share” of the informatics team. This is an annual commitment for a fraction of an informaticist and will cost $960/mo for an average of 4h/week of informatics support. The monthly usage levels do not have to be exact and can be used in large blocks. The hours in the share can be used with any member of the team and the informaticist can vary from project to project.  <BR><BR>
We hope this change will make accessing the [[BioMicroCenter:RTPCR|RT-PCR]] machines easier and will also create room for the [[BioMicroCenter:Tecan_Freedom_Evo|new Tecan EVO 150]], scheduled to arrive in early June. Keep an eye on this page for future updates!
+
Finally, and importantly, we will be changing the way we are storing Illumina sequencing data long term. In the past, we have saved the fastq, sam and bam files, along with the quality control data, in a zipped file. These zipped files now occupy over 50TB of storage which is limiting  how we are able to handle new sequencing runs. To address this, we will be deleting the fastq and sam files from the archive and storing only the binary bam and quality control files. The fastq and sam files can be regenerated rapidly from the bam files using Picard and SamTools (though reads may not be in the same order). As always, we strongly encourage you to keep your own copy of the Illumina data and use our version only as a backup. We will begin this conversion next week.
 +
If you have any concerns, please do not hesitate to contact me.
  
=== April 19, 2010 ===
 
  
Starting next month, the [http://mit.edu/ki/index.html Koch Institute] and the MIT BioMicro Center will be hosting a [http://www.nanostring.com/ Nanostring] nCounter system on a trial basis. The [http://www.nanostring.com/products/ncounter/ nCounter system] is a [http://www.nanostring.com/applications/technology/ single molecule visualizer] that quantitatively detects RNA and other nucleic acids using a hybridization system in a highly multiplex manner. The system uses color-coded molecular barcodes to digitally count nucleic acid molecules in solution. The system does not use enzymes for detecting the nucleic acids, allowing direct measurements of mRNA from a variety of input materials including degraded RNA or crude cell lysates.
 
  
The instruments will be located in the BioMicro Center and will be available to all members of the MIT community. We will be using this time to gauge the level of interest in the nCounter and whether it would be a viable system to purchase.
 
  
If you are interested in learning more, we will be hosting a seminar with [http://www.nanostring.com/ Nanostring] representatives on April 30th. The seminar will be at 11am in 68-181. Nanostring representatives will be available after the talk to discuss the instruments and specific applications. More information is in the [[Media:Nanostring_abstract.pdf‎|ABSTRACT]] for the talk.
+
|valign="top"|
  
=== April 1, 2010 ===
+
== PUBLICATIONS ==
 
+
'''2013'''<BR><BR>
Thanks to the generosity of a grant from the [http://www.moore.org/ Moore Foundation] to Dr. Penny Chisholm and ARRA funding to Dr. Chris Burge the BioMicro Center will be significantly expanding our sequencing capacity over the next 4-6 months. The first step of this expansion begins today with the addition of a new [http://www.illumina.com/systems/genome_analyzer_iix.ilmn GAIIx] and [http://www.illumina.com/systems/genome_analyzer/cbot.ilmn cBot] from Illumina. We are working hard to get ''"Ryland"'' and ''"Agustus Gloop"'' up and running and we hope to be able to shorten our queue times very soon!
+
'''2012'''<BR><BR>
 
+
<biblio>
=== March 2010 ===
+
#Paper1 pmid=22981692 <!-SL Boyer: Heart->
Due to an increase in the cost of Illumina reagents, increase in data file size, and the complexity of sample preps, we have had to increase, slightly, the cost of Illumina sequencing. These new rates will be effective on samples submitted after April 1, 2010. Samples already in the queue will use the current rates.
+
#Paper2 pmid=22847430 <!-SL Saeij->
 
+
#Paper3 pmid=22102570 <!-HD Chisholm->
{| border=1 align="right"
+
</biblio>
! ILLUMINA SEQUENCING
+
'''2011'''<BR><BR>
!width=100| MIT - current
+
<biblio>
!width=100| MIT - April 1, 2010
+
#Paper1 pmid=21892155 <!-SL Sur->
!width=100| unit
+
</biblio>
! Notes
+
'''2010'''<BR><BR>
|-
+
<biblio>
| Single End (36nt)
+
#Paper1 pmid=20720539 <!-SL Young->
|align="right"| $805
+
#Paper2 pmid=20581084 <!-SL Zwaka->
|align="right"| $860
+
</biblio>
|align="center"| per lane
+
'''2009'''<BR><BR>
| inlcudes quality control (RT-PCR or BioAnalyzer), sequencing, genome alignment and data storage of Firecrest files for 2 yrs.
+
<biblio>
|-
+
#Paper1 pmid=19531355 <!-SL Amon->
| Paired End (36+36nt)
+
</biblio>
|align="right"| $1,385
 
|align="right"| $1,450
 
|align="center"| per lane
 
|
 
|-
 
| Add'l 36nt
 
|align="right"| $295
 
|align="right"| $300
 
|align="center"| per lane
 
 
|-
 
| Sample Multiplexing
 
|align="right"| $0
 
|align="right"| $50
 
|align="center"| per 10 samples combined
 
| Combined over the whole order. Only applies to samples combined by BCM technicians.
 
|-
 
| Repriming
 
|align="right"| $200
 
|align="right"| $300
 
|align="center"| per flow cell
 
| Uses 6nt. Cost is divided by number of lanes requiring repriming. Repriming is required for standard Illumina multiplexing.
 
|-
 
|}
 
<BR>
 
Non-MIT rates are 30% higher for academic institutions and 50% highers for non-academic institutions. Priority is given to samples from CORE facilities.
 
 
 
 
 
|-
 
|valign="top" width="45%"|
 
 
 
<B><BIG>PREVIOUS NEWSLETTERS </BIG></B>
 
  
 +
== PREVIOUS NEWSLETTERS ==
  
 +
'''[[BioMicroCenter:News2012|2012]]'''<BR>
 +
'''[[BioMicroCenter:News2011|2011]]'''<BR>
 
'''[[BioMicroCenter:News2010|2010]]'''
 
'''[[BioMicroCenter:News2010|2010]]'''
 +
<br>
  
<br>
+
== RECENT CHANGES TO THE WEBSITE ==
<B><BIG>RECENT CHANGES TO THE WEBSITE <\BIG><\B>
 
 
{{BioMicroChanges}}
 
{{BioMicroChanges}}
  
 
|}
 
|}

Revision as of 19:16, 11 January 2013

BioMicroCenter-header6.jpg

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

BioMicro Center News

JANUARY 9, 2013

Happy new years to everyone. A couple new things happening in BioMicro that we want to make everyone aware of.

First, this month begins a year long experiment in joining the BioMicro Center Informatics team and the KI Bioinformatics and Computing Core in to a single team. Our two teams have been collaborating for several years, sharing computational infrastructure, etc. but this year we will be formalizing and expanding the relationship with the goal of creating a more efficient unified core. Informatics analysis requests should still be sent to Charlie Whittaker or to myself as usual, but will be spread across the joint team based on expertise and on availability. You are also, as always, welcome to contact any of the informatics scientists directly. We hope this will allow us to reduce waiting times and to keep costs under control.

During the trial period (and hopefully going forward), pricing for informatics will be available in two flavors. First, for projects needing routine work, the subsidized rate will be $70/h for all CORE members (Biology, BE, KI, CEHS). For more involved projects, we have second option to purchase a “share” of the informatics team. This is an annual commitment for a fraction of an informaticist and will cost $960/mo for an average of 4h/week of informatics support. The monthly usage levels do not have to be exact and can be used in large blocks. The hours in the share can be used with any member of the team and the informaticist can vary from project to project.

Finally, and importantly, we will be changing the way we are storing Illumina sequencing data long term. In the past, we have saved the fastq, sam and bam files, along with the quality control data, in a zipped file. These zipped files now occupy over 50TB of storage which is limiting how we are able to handle new sequencing runs. To address this, we will be deleting the fastq and sam files from the archive and storing only the binary bam and quality control files. The fastq and sam files can be regenerated rapidly from the bam files using Picard and SamTools (though reads may not be in the same order). As always, we strongly encourage you to keep your own copy of the Illumina data and use our version only as a backup. We will begin this conversion next week. If you have any concerns, please do not hesitate to contact me.



PUBLICATIONS

2013

2012

  1. Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, and Bruneau BG. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 2012 Sep 28;151(1):206-20. DOI:10.1016/j.cell.2012.07.035 | PubMed ID:22981692 | HubMed [Paper1]
  2. Minot S, Melo MB, Li F, Lu D, Niedelman W, Levine SS, and Saeij JP. Admixture and recombination among Toxoplasma gondii lineages explain global genome diversity. Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13458-63. DOI:10.1073/pnas.1117047109 | PubMed ID:22847430 | HubMed [Paper2]
  3. Kelly L, Huang KH, Ding H, and Chisholm SW. ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage. Nucleic Acids Res. 2012 Jan;40(Database issue):D632-40. DOI:10.1093/nar/gkr1022 | PubMed ID:22102570 | HubMed [Paper3]
All Medline abstracts: PubMed | HubMed

2011

  1. Mellios N, Sugihara H, Castro J, Banerjee A, Le C, Kumar A, Crawford B, Strathmann J, Tropea D, Levine SS, Edbauer D, and Sur M. miR-132, an experience-dependent microRNA, is essential for visual cortex plasticity. Nat Neurosci. 2011 Sep 4;14(10):1240-2. DOI:10.1038/nn.2909 | PubMed ID:21892155 | HubMed [Paper1]

2010

  1. Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, Ebmeier CC, Goossens J, Rahl PB, Levine SS, Taatjes DJ, Dekker J, and Young RA. Mediator and cohesin connect gene expression and chromatin architecture. Nature. 2010 Sep 23;467(7314):430-5. DOI:10.1038/nature09380 | PubMed ID:20720539 | HubMed [Paper1]
  2. Dejosez M, Levine SS, Frampton GM, Whyte WA, Stratton SA, Barton MC, Gunaratne PH, Young RA, and Zwaka TP. Ronin/Hcf-1 binds to a hyperconserved enhancer element and regulates genes involved in the growth of embryonic stem cells. Genes Dev. 2010 Jul 15;24(14):1479-84. DOI:10.1101/gad.1935210 | PubMed ID:20581084 | HubMed [Paper2]
All Medline abstracts: PubMed | HubMed

2009

  1. Boselli M, Rock J, Unal E, Levine SS, and Amon A. Effects of age on meiosis in budding yeast. Dev Cell. 2009 Jun;16(6):844-55. DOI:10.1016/j.devcel.2009.05.013 | PubMed ID:19531355 | HubMed [Paper1]

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2012
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