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== Welcome to the MIT BIOMICRO CENTER ==


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== BioMicro Center News ==
=== JULY 2017 ===
We have several exciting developments to tell you about over the next few months. This month, we have some major changes in our QC with the addition of an [[BioMicroCenter:FemtoPulse|AATI FemtoPulse]] and an upgrade of the [[BioMicroCenter:Advanced_analytical_Fragment_analyzer| AATI Fragment Analyzer]]. <BR><BR>


=== Nov 9, 2010 ===
[[BioMicroCenter:FemtoPulse|AATI FemtoPulse]] is a redesigned version of the Fragment Analyzer that significantly expands its capabilities. The new instrument can detect nucleic acid down to concentrations of 5 fg/ul – approximately 5000 molecules of a 1kb fragment. In addition, it will incorporate a pulse field generator allowing it to separate fragments of over 200kb. Advanced Analytical has provided us an early instrument in the hope of identifying novel applications that require this extreme sensitivity. The Femto Pulse was donated to the BioMicro Center by the MIT Center for Environmental Health Sciences. We will be scheduling a Technology Seminar to introduce the FemtoPulse in the fall.<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>


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>
Next week we will also be upgrading our [[BioMicroCenter:Advanced_analytical_Fragment_analyzer|AATI Fragment Analyzer]] from a 12 capillary to a 48 capillary machine to address consistent and increasing backlogs on the instrument. This expanded capacity will allow us to batch many more samples on each run. A side effect of this upgrade is we will need to likely move some smaller projects back to the Agilent BioAnalyzer to avoid wasting reagents.  For the moment, we will not be adjusting the rates of batched samples.<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.  
Deployment of the Femto Pulse and upgrade of the Fragment Analyzer will occur this coming Monday to Wednesday. During this time, there may be some delays while the instruments are installed and serviced. We will also use this time to upgrade the iLab sample submission system, so we ask for your patience while we roll these changes out.<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>
=== APRIL 2017 ===
We have used the sunsetting of the [[BioMicroCenter:Neoprep|Illumina Neoprep]] as an opportunity to re-evaluate all of our library prep methodologies with an eye on significantly reducing library preparation costs. We’re now ready to roll out hand preparation for these methods as well as some of our automation to help smooth the transition. We plan to bring in scientists from the different manufacturers we’ve been looking at through our Technology Seminar Series to answer any questions you may have. For all of the methods, we will have a single sample price as well as a batch price that will be significantly cheaper per sample. Below are the RNAseq methods that are already locked in.
{|border="1"
|Method / Kit
|Per sample ||Per 24 ||Per 96 / 384
|-
|polyA RNA (>50ng):<BR>Kapa Hyperprep
|$150 ||$2,000 (est) ||NA
|-
|3’Digital Gene Expression
|NA ||$1,200 ||$4,000
|-
|Ribosomal Depletion (human/mouse):<BR>Kapa RiboGone
|$225 || TBD || TBD
|-
|Ribosomal Depletion (other):<BR>Illumina Ribozero + Kapa Hyperprep
|$250 || TBD || NA
|-
|Low input polyA:<BR>Clontech SMARTseq v4
|$300 || $1,600 || $2,500 / $5,000
|-
|Low input ribosomal depletion (human/mouse) <BR> Clontech ZapR kit
|$200 || TBD || TBD
|}
Please note that we do not consider this problem ‘solved’ and we are continuing to work on adapting new protocols with the aim of lowering cost while maintaining quality. We also are not yet complete with the process of getting everything listed in iLabs which will happen over the next couple weeks. The Neoprep will be shut down on July 31.<BR><BR>


-Stuart Levine
A second area we continue to address is data storage.  With recent expansions to the systems, we are able to significantly lower our data storage costs for next year. Active storage will now be $200/TB/y while archival storage (read only) will be at $100/TB/y.<BR><BR>


=== Sep 12, 2010 ===
Finally, many of you may have heard about a recent issue of “index switchng” or “pad swapping” on Illumina sequencers from a bioRxiv preprint from Stanford or social media (http://biorxiv.org/content/early/2017/04/09/125724). We have been well aware of this issue for many years and that it is endemic in all Illumina sequencers (we called it “barcode swapping” in house). Fortunately for us, the non-patterned flowcells (such as MiSeq, NextSeq and HiSeq2000) have a significantly lower issue with this than the newer instruments. Even so, the low level of index switching we have observed (~0.1% of reads for most runs) is a primary reason we have resisted mixing libraries from different labs on single sequencing lanes. If you have any questions/concerns about this instrument ‘feature’, we are happy to discuss it with you. Our hope is the new emphasis on this issue for the patterned flowcells will result in improved methodologies that further lower the likelihood of barcode swaps.  
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


=== JANUARY 2017 ===
BMC is officially moving almost all of our sample intake to [https://mit.ilabsolutions.com iLabs]. We have spent the past several months moving the forms for Illumina library prep, sequencing and Pacbio sequencing over to the new system and testing it out - thank you to the labs that helped us with our beta testing! You can find BMC in iLabs at https://mit.ilabsolutions.com/ in the KI Genomics Core / MIT BioMicro Center section. The new forms are under "Request Services". All projects using MIT cost objects should use iLabs going forward. Projects being billed to outside groups or by PO should continue to use the forms on the website.<BR><BR>


=== Aug 9, 2010 ===
The [[BioMicroCenter:Covaris|Covaris E220]] is now up and running. We will be having a [[BioMicroCenter:Technology_Seminar_Series|seminar for it on January 11th]] (details TBA). Our Covaris rep will be on hand that day to help you set up your protocols as well. Please let Jon or myself know if you would like to schedule time. There is no charge for this retraining. <BR><BR>
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====
The price for SYBR green is decreasing significantly to $25/ml. In the fall, we compared a number of new providers based on their ability to quantify Illumina libraries. Of the two we tested, one preformed as well as KAPA (the other did not). KAPA, in turn, was able to lower the cost of their SYBR significantly which we prefer as it will maintain consistency. Due to the lower cost, we are also removing the pooling charges from Illumina sequencing - those costs are being absorbed into the QC costs instead. The Roche SYBR did not match this lower cost and we will be discontinuing our bulk purchases of it.<BR><BR>
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 ===
Finally, we are introducing a significantly cheaper library prep for [[BioMicroCenter:DNA_HTL|very high-throughput experiments]]. We have been collaborating closely with [http://ttplabtech.com/liquid-handling/mosquito_hv/ TTP Labtech to adapt their Mosquito] liquid handler for core facility settings. Our first method is NexteraXT. Using the Mosquito, we have been able to reduce the reaction volume by an order of magnitude. A 96 well plate will cost <$15/sample and a 384 well plate is under $7.50/sample. These new methods are ideally suited for single cell and amplicon work but are NOT well suited for de novo assembly as the library complexity is lower due to the lower amount of input DNA. TTP will be giving the [[BioMicroCenter:Technology_Seminar_Series|seminar in February]].
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:
* The freezers have been relocated to the 304 hallway
* The RT-PCR machines will be moving to the 316 entry.
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!


=== 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.
|valign="top"|


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.
== ABOUT THE BIOMICRO CENTER ==


=== April 1, 2010 ===
The MIT BioMicro Center was founded in 2000 as the core bio-fabrication and microarray processing facility at MIT. The Center is a joint endeavor between the [http://biology.mit.edu Department of Biology], the [http://ki.mit.edu Koch Institute for Integrative Cancer Research], the [http://be.mit.edu Department of Biological Engineering] and the [http://cehs.mit.edu MIT Center for Environmental Health Sciences.] The BioMicro Center offers a wide range of genomic services to researchers at MIT. The majority of services rendered pertain to massively parallel sequencing using the Illumina platform (both library preparation and sequencing). Commercial array processing and include both the Affymetrix Gene Chip and Agilent DNA array platforms are also part of our portfolio. Real-time PCR and Agilent BioAnalyzer services are available in the facility both as services available to researchers, as well as for quality control of microarray and sequencing samples. In addition, the Center has a presence in high-throughput screening with robotics and plate reading as well as informatics and computational support. The BioMicro Center serves the [http://ki.mit.edu Koch Institute] as the [http://ki.mit.edu/sbc/microarray MicroArray Technologies Core] and as part of the [http://ki.mit.edu/sbc/bioinformatics Bioinformatics and Computing Core] and the [http://cehs.mit.edu MIT Center for Environmental Health Sciences] as part of the [http://cehs.mit.edu/facilities.html#Genomics_and_Bioinformatics_Core Genomics and Imaging Core]<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!
Experimental and analytical work done in the BioMicro Center is funded by the NIH and must be made available through the NIH's open access policy. All Koch Institute and CEHS labs '''must''' acknowledge their core grants for work done in the core with the following language.  
* KI ''"This work was funded by the National Cancer Institute of the NIH under award P30-CA14051"''  
* [[BioMicroCenter:CEHS13|CEHS]] ''"This work was funded by the National Institute of Environmental Health Sciences of the NIH under award P30-ES002109"''


=== March 2010 ===
== PUBLICATIONS ==
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.
Please note the publication aspect of OWW is not working. This section is disabled.
<!--
'''2015'''<BR><BR>
<biblio>
#Paper1 pmid=25837992 <!- SL.JW Essig->
#Paper2 pmid=25477501 <!- VB Boyer->
#Paper3 pmid=25561496 <!- AJ Sharp->
#Paper4 pmid=26163349 <!- HD.CW Hynes->
#Paper5 pmid=26341558 <!- AJ.CW Gertler Jacks->
#Paper6 pmid=26510153 <!- VB Saeij->
#Paper7 pmid=26522011 <!- HD Chisholm->
</biblio>
'''2014'''<BR><BR>
<biblio>
#Paper1 pmid=24501120 <!- RPA Walker->
#Paper2 pmid=24501121 <!- RPA Walker->
#Paper3 pmid=24249727 <!- VB Saeij->
#Paper4 pmid=24757057 <!- RPA.VB Samson->
#Paper5 pmid=24763590 <!- HD Chisholm->
#Paper6 pmid=24899568  <!- VB.SL Dedon->
#Paper7 pmid=24931974 <!- VB Burge->
#Paper8 pmid=24413286 <!- RPA.SL Tannenbaum Fox->
#Paper9 pmid=25333635 <!- VB.SL Boyer->
#Paper10 pmid=25197050 <!- JW.CW Amon->
#Paper11 pmid=25037231 <!- CW Hynes->
#Paper12 pmid=25337879 <!- AJ Jacks->
#Paper13 pmid=24954536 <!- AJ Jacks2->
#Paper14 pmid=24788094 <!- AJ Sharp->
#Paper15 pmid=24711431 <!- AJ Jacks3->
#Paper16 pmid=24630729 <!- AJ Jacks4->
#Paper17 pmid=25477501 <!- VB Boyer2->
#Paper18 pmid=25348403 <!- RPA.SL Dedon ->


{| border=1 align="right"
 
! ILLUMINA SEQUENCING
</biblio>
!width=100| MIT - current
!width=100| MIT - April 1, 2010
!width=100| unit
! Notes
|-
| Single End (36nt)
|align="right"| $805
|align="right"| $860
|align="center"| per lane
| inlcudes quality control (RT-PCR or BioAnalyzer), sequencing, genome alignment and data storage of Firecrest files for 2 yrs.
|-
| Paired End (36+36nt)
|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.


'''2013'''<BR><BR>
<biblio>
#Paper1 pmid=23662897 <!- BMC Paper->
#Paper2 pmid=23657361 <!- HD Chisholm->
#Paper3 pmid=23352431 <!- HD.VB Boyer->
#Paper4 pmid=23630078 <!- CW.AJ Sharp->
#Paper5 pmid=23523371 <!- CW Jacks->
#Paper6 pmid=23990805 <!- SL.VB Boyer->
#Paper7 pmid=24009526 <!- CW Lees->
#Paper8 pmid=23873940 <!- CW Jacks2->
#Paper10 pmid=24134150 <!- SL.RPA Tannenbaum->
#Paper11 pmid=24367253 <!- VB Saeij->
#Paper12 pmid=23703590 <!- SM Fraenkel ->
</biblio>
'''2012'''<BR><BR>
<biblio>
#Paper1 pmid=22981692 <!-SL Boyer: Heart->
#Paper2 pmid=22847430 <!-SL Saeij->
#Paper3 pmid=22102570 <!-HD Chisholm->
</biblio>
'''2011'''<BR><BR>
<biblio>
#Paper1 pmid=21892155 <!-SL Sur->
</biblio>
'''2010'''<BR><BR>
<biblio>
#Paper1 pmid=20720539 <!-SL Young->
#Paper2 pmid=20581084 <!-SL Zwaka->
</biblio>
'''2009'''<BR><BR>
<biblio>
#Paper1 pmid=19531355 <!-SL Amon->
</biblio>


|-
-->
|valign="top" width="45%"|
 
<B><BIG>PREVIOUS NEWSLETTERS </BIG></B>
 


== PREVIOUS NEWSLETTERS ==
'''[[BioMicroCenter:News2016|2016]]'''<BR>
'''[[BioMicroCenter:News2015|2015]]'''<BR>
'''[[BioMicroCenter:News2014|2014]]'''<BR>
'''[[BioMicroCenter:News2013|2013]]'''<BR>
'''[[BioMicroCenter:News2012|2012]]'''<BR>
'''[[BioMicroCenter:News2011|2011]]'''<BR>
'''[[BioMicroCenter:News2010|2010]]'''
'''[[BioMicroCenter:News2010|2010]]'''
<br>


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== RECENT CHANGES TO THE WEBSITE ==
<B><BIG>RECENT CHANGES TO THE WEBSITE <\BIG><\B>
{{BioMicroChanges}}
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|}
|}

Revision as of 11:39, 21 July 2017

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

.

Welcome to the MIT BIOMICRO CENTER

BioMicro Center News

JULY 2017

We have several exciting developments to tell you about over the next few months. This month, we have some major changes in our QC with the addition of an AATI FemtoPulse and an upgrade of the AATI Fragment Analyzer.

AATI FemtoPulse is a redesigned version of the Fragment Analyzer that significantly expands its capabilities. The new instrument can detect nucleic acid down to concentrations of 5 fg/ul – approximately 5000 molecules of a 1kb fragment. In addition, it will incorporate a pulse field generator allowing it to separate fragments of over 200kb. Advanced Analytical has provided us an early instrument in the hope of identifying novel applications that require this extreme sensitivity. The Femto Pulse was donated to the BioMicro Center by the MIT Center for Environmental Health Sciences. We will be scheduling a Technology Seminar to introduce the FemtoPulse in the fall.

Next week we will also be upgrading our AATI Fragment Analyzer from a 12 capillary to a 48 capillary machine to address consistent and increasing backlogs on the instrument. This expanded capacity will allow us to batch many more samples on each run. A side effect of this upgrade is we will need to likely move some smaller projects back to the Agilent BioAnalyzer to avoid wasting reagents. For the moment, we will not be adjusting the rates of batched samples.

Deployment of the Femto Pulse and upgrade of the Fragment Analyzer will occur this coming Monday to Wednesday. During this time, there may be some delays while the instruments are installed and serviced. We will also use this time to upgrade the iLab sample submission system, so we ask for your patience while we roll these changes out.

APRIL 2017

We have used the sunsetting of the Illumina Neoprep as an opportunity to re-evaluate all of our library prep methodologies with an eye on significantly reducing library preparation costs. We’re now ready to roll out hand preparation for these methods as well as some of our automation to help smooth the transition. We plan to bring in scientists from the different manufacturers we’ve been looking at through our Technology Seminar Series to answer any questions you may have. For all of the methods, we will have a single sample price as well as a batch price that will be significantly cheaper per sample. Below are the RNAseq methods that are already locked in.

Method / Kit Per sample Per 24 Per 96 / 384
polyA RNA (>50ng):
Kapa Hyperprep 		$150 $2,000 (est) NA
3’Digital Gene Expression NA $1,200 $4,000
Ribosomal Depletion (human/mouse):
Kapa RiboGone 		$225 TBD TBD
Ribosomal Depletion (other):
Illumina Ribozero + Kapa Hyperprep 		$250 TBD NA
Low input polyA:
Clontech SMARTseq v4 		$300 $1,600 $2,500 / $5,000
Low input ribosomal depletion (human/mouse)
Clontech ZapR kit 		$200 TBD TBD

Please note that we do not consider this problem ‘solved’ and we are continuing to work on adapting new protocols with the aim of lowering cost while maintaining quality. We also are not yet complete with the process of getting everything listed in iLabs which will happen over the next couple weeks. The Neoprep will be shut down on July 31.

A second area we continue to address is data storage. With recent expansions to the systems, we are able to significantly lower our data storage costs for next year. Active storage will now be $200/TB/y while archival storage (read only) will be at $100/TB/y.

Finally, many of you may have heard about a recent issue of “index switchng” or “pad swapping” on Illumina sequencers from a bioRxiv preprint from Stanford or social media (http://biorxiv.org/content/early/2017/04/09/125724). We have been well aware of this issue for many years and that it is endemic in all Illumina sequencers (we called it “barcode swapping” in house). Fortunately for us, the non-patterned flowcells (such as MiSeq, NextSeq and HiSeq2000) have a significantly lower issue with this than the newer instruments. Even so, the low level of index switching we have observed (~0.1% of reads for most runs) is a primary reason we have resisted mixing libraries from different labs on single sequencing lanes. If you have any questions/concerns about this instrument ‘feature’, we are happy to discuss it with you. Our hope is the new emphasis on this issue for the patterned flowcells will result in improved methodologies that further lower the likelihood of barcode swaps.

JANUARY 2017

BMC is officially moving almost all of our sample intake to iLabs. We have spent the past several months moving the forms for Illumina library prep, sequencing and Pacbio sequencing over to the new system and testing it out - thank you to the labs that helped us with our beta testing! You can find BMC in iLabs at https://mit.ilabsolutions.com/ in the KI Genomics Core / MIT BioMicro Center section. The new forms are under "Request Services". All projects using MIT cost objects should use iLabs going forward. Projects being billed to outside groups or by PO should continue to use the forms on the website.

The Covaris E220 is now up and running. We will be having a seminar for it on January 11th (details TBA). Our Covaris rep will be on hand that day to help you set up your protocols as well. Please let Jon or myself know if you would like to schedule time. There is no charge for this retraining.

The price for SYBR green is decreasing significantly to $25/ml. In the fall, we compared a number of new providers based on their ability to quantify Illumina libraries. Of the two we tested, one preformed as well as KAPA (the other did not). KAPA, in turn, was able to lower the cost of their SYBR significantly which we prefer as it will maintain consistency. Due to the lower cost, we are also removing the pooling charges from Illumina sequencing - those costs are being absorbed into the QC costs instead. The Roche SYBR did not match this lower cost and we will be discontinuing our bulk purchases of it.

Finally, we are introducing a significantly cheaper library prep for very high-throughput experiments. We have been collaborating closely with TTP Labtech to adapt their Mosquito liquid handler for core facility settings. Our first method is NexteraXT. Using the Mosquito, we have been able to reduce the reaction volume by an order of magnitude. A 96 well plate will cost <$15/sample and a 384 well plate is under $7.50/sample. These new methods are ideally suited for single cell and amplicon work but are NOT well suited for de novo assembly as the library complexity is lower due to the lower amount of input DNA. TTP will be giving the seminar in February.


ABOUT THE BIOMICRO CENTER

The MIT BioMicro Center was founded in 2000 as the core bio-fabrication and microarray processing facility at MIT. The Center is a joint endeavor between the Department of Biology, the Koch Institute for Integrative Cancer Research, the Department of Biological Engineering and the MIT Center for Environmental Health Sciences. The BioMicro Center offers a wide range of genomic services to researchers at MIT. The majority of services rendered pertain to massively parallel sequencing using the Illumina platform (both library preparation and sequencing). Commercial array processing and include both the Affymetrix Gene Chip and Agilent DNA array platforms are also part of our portfolio. Real-time PCR and Agilent BioAnalyzer services are available in the facility both as services available to researchers, as well as for quality control of microarray and sequencing samples. In addition, the Center has a presence in high-throughput screening with robotics and plate reading as well as informatics and computational support. The BioMicro Center serves the Koch Institute as the MicroArray Technologies Core and as part of the Bioinformatics and Computing Core and the MIT Center for Environmental Health Sciences as part of the Genomics and Imaging Core

Experimental and analytical work done in the BioMicro Center is funded by the NIH and must be made available through the NIH's open access policy. All Koch Institute and CEHS labs must acknowledge their core grants for work done in the core with the following language.

  • KI "This work was funded by the National Cancer Institute of the NIH under award P30-CA14051"
  • CEHS "This work was funded by the National Institute of Environmental Health Sciences of the NIH under award P30-ES002109"

PUBLICATIONS

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25 April 2024

      00:22  The paper that launched microfluidics - Xi Ning‎‎ 7 changes history +4,723‎ [Xning098‎ (7×)]
     
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00:18 (cur | prev) +14‎ Xning098 talk contribs (→‎Summary)
     
00:11 (cur | prev) +1‎ Xning098 talk contribs (→‎Introduction)
     
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00:11 (cur | prev) 0‎ Xning098 talk contribs (→‎References)
     
00:08 (cur | prev) +4‎ Xning098 talk contribs (→‎Significance)
     
00:07 (cur | prev) +4,800‎ Xning098 talk contribs

24 April 2024

      22:50  WAKNA:Basics‎‎ 8 changes history +610‎ [Berthold Drexler‎ (8×)]
     
22:50 (cur | prev) +136‎ Berthold Drexler talk contribs (→‎Hier finden Sie Literatur für Einsteiger:innen in das Gebiet der Neuroanästhesie)
     
22:47 (cur | prev) +238‎ Berthold Drexler talk contribs (→‎Neuromonitoring allgemein)
     
22:33 (cur | prev) +151‎ Berthold Drexler talk contribs (→‎Hier finden Sie Literatur für Einsteiger:innen in das Gebiet der Neuroanästhesie)
     
22:31 (cur | prev) 0‎ Berthold Drexler talk contribs (→‎Grundlagen, Physiologie & Pharmakologie)
     
22:30 (cur | prev) +1‎ Berthold Drexler talk contribs (→‎Grundlagen, Physiologie & Pharmakologie)
     
22:30 (cur | prev) +313‎ Berthold Drexler talk contribs (→‎Grundlagen, Physiologie & Pharmakologie)
     
06:23 (cur | prev) +192‎ Berthold Drexler talk contribs (→‎Hier finden Sie Literatur für Einsteiger:innen in das Gebiet der Neuroanästhesie)
     
06:21 (cur | prev) −421‎ Berthold Drexler talk contribs (→‎Sonstige)
     18:35  User:Yanbin Huang‎‎ 2 changes history +25‎ [Yanbin Huang‎ (2×)]
     
18:35 (cur | prev) +13‎ Yanbin Huang talk contribs (→‎Peer-Reviewed Publications)
     
18:34 (cur | prev) +12‎ Yanbin Huang talk contribs (→‎Peer-Reviewed Publications)
     17:49  Hu‎‎ 2 changes history +28‎ [Hugangqing‎ (2×)]
     
17:49 (cur | prev) +18‎ Hugangqing talk contribs
     
17:48 (cur | prev) +10‎ Hugangqing talk contribs
     08:14  "Pick and Place" Assembly of Parts Using PDMS - Amy Lim, Rylie Costello‎‎ 6 changes history +394‎ [Rcostello‎ (6×)]
     
08:14 (cur | prev) +1‎ Rcostello talk contribs (→‎"Pick and Place" Methodology)
     
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08:12 (cur | prev) +110‎ Rcostello talk contribs (→‎References)
     
08:11 (cur | prev) +299‎ Rcostello talk contribs (→‎"Pick and Place" Methodology)
     08:02 Upload log Rcostello talk contribs uploaded File:Pick and Place.mp4 ‎

23 April 2024

      15:33  "Pick and Place" Assembly of Parts Using PDMS - Amy Lim, Rylie Costello‎‎ 6 changes history +837‎ [Rcostello‎ (6×)]
     
15:33 (cur | prev) +1‎ Rcostello talk contribs (→‎"Pick and Place" for Microfluidics)
     
15:33 (cur | prev) +203‎ Rcostello talk contribs (→‎References)
     
15:31 (cur | prev) −2‎ Rcostello talk contribs (→‎"Pick and Place" for Microfluidics)
     
15:29 (cur | prev) −474‎ Rcostello talk contribs (→‎References)
     
15:29 (cur | prev) +845‎ Rcostello talk contribs (→‎MEMS Devices)
     
15:14 (cur | prev) +264‎ Rcostello talk contribs (→‎"Pick and Place" for Microfluidics)
     11:58  BioMicroCenter:People‎‎ 2 changes history +30‎ [Lttran‎ (2×)]
     
11:58 (cur | prev) −4‎ Lttran talk contribs (→‎BioMicro Center Staff)
     
11:49 (cur | prev) +34‎ Lttran talk contribs (→‎BioMicro Center Staff)
     11:46 Upload log Lttran talk contribs uploaded File:SKR BMC.jpg ‎

22 April 2024

      19:28  "Pick and Place" Assembly of Parts Using PDMS - Amy Lim, Rylie Costello‎‎ 2 changes history −2‎ [Rcostello‎ (2×)]
     
19:28 (cur | prev) −2‎ Rcostello talk contribs (→‎Nanowires)
     
19:26 (cur | prev) 0‎ Rcostello talk contribs (→‎Biology-Inspired Solution)
     19:01  Microfluidic Sensing- Microfluidic Biosensors- Xiao Fan‎‎ 13 changes history +131‎ [Khiemle‎ (13×)]
     
19:01 (cur | prev) +14‎ Khiemle talk contribs (→‎Microfluidic immunosensors)
     
19:00 (cur | prev) +7‎ Khiemle talk contribs (→‎DNA-based microfluidic biosensors)
     
19:00 (cur | prev) +18‎ Khiemle talk contribs (→‎Microfluidic immunosensors)
     
18:59 (cur | prev) +18‎ Khiemle talk contribs (→‎Microfluidic immunosensors)
     
18:58 (cur | prev) −2‎ Khiemle talk contribs (→‎DNA-based microfluidic biosensors)
     
18:58 (cur | prev) +2‎ Khiemle talk contribs (→‎Enzyme-based microfluidic biosensors)
     
18:58 (cur | prev) +1‎ Khiemle talk contribs (→‎Enzyme-based microfluidic biosensors)
     
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18:57 (cur | prev) +2‎ Khiemle talk contribs (→‎DNA-based microfluidic biosensors)
     
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18:56 (cur | prev) +86‎ Khiemle talk contribs (→‎Microfluidic immunosensors)
     
18:54 (cur | prev) 0‎ Khiemle talk contribs (→‎Enzyme-based microfluidic biosensors)
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