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== BioMicro Center News ==
== BioMicro Center News ==
=== JUNE 2015 ===
=== JULY 2017 ===
Hello everyone,
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>
A couple of updates from the BioMicro Center to let you know about as we begin summer.  
* '''Microarrays:''' Starting in July, we will be phasing out our Agilent microarray service. The demand for this platform has been very weak and the vendor support has been even weaker. We will continue to maintain the scanner for walkup service but labeling and hybridization services will be done on a custom basis only. [[BioMicroCenter:Microarrays|Affymetrix]] services will continue, and will even [[BioMicroCenter:PricingFY2016|decrease in price significantly]] as the company has provided us with very aggressive pricing for the next year. A list of prices for the next year is on our website.


* '''Bioinformatics:''' We have begun a monthly training series in informatics for our core researchers. We are still in the pilot phase and definitely have some kinks to work out as we introduce these new classes. The classes will alternate between basic introductions and more advanced topics but will generally be in the afternoon on the second Monday of each month. [[BioMicroCenter:People|Duan Ma]] will be leading this effort. You can find the calendar on [[BioMicroCenter:BioinfoClasses|our website.]]
[[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>


* '''Sequencing:''' We are making a few tweaks to the pricing for Illumina sequencing – all in the down direction.  The initial reprime for index reads on the HiSeq will now be included in the price of the lane. Additionally, multiplex costs will be removed for all libraries prepped by the BMC.
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>
* We are continuing to work closely with Illumina on the ongoing challenges with read quality for long MiSeq runs. The issues have been traced to the sequencing reagents and we are aware Illumina is working aggressively on a solution. However, there is still no timeline on a fix yet. 250PE and particularly 300PE MiSeq runs should be done cautiously.  
<BR><BR>
Finally, a couple personnel changes to know about. Fangming and Jonathan will be rotating off in a couple weeks. We are bringing their replacements, Rachel and Rob, up to speed now and they’ll be ready by July. We also are welcoming [BioMicroCenter:People|Vidya Subramanian] on board as our new technology development specialist. She will be focusing initially on bringing new library preparation methodologies into the BioMicro Center.


=== OCTOBER 2014 ===
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 role these changes out.<BR><BR>
A number of very important announcements from BioMicro Center this month. More details are on our website.<BR>
* We have added our newest sequencer: The [[BioMicroCenter:Sequencing#NextSeq|Illumina NextSeq500.]] The NextSeq is built as a very powerful MiSeq; using a single sample flowcell and processing a base every 5 minutes, but produces 400m reads per run.  The system can produce 30x mammalian genomes in a couple days with read lengths up to 150 paired end. The NextSeq was funded by Doug Laufenburger, Penny Chisholm, the KI and the Dept of Biology. Note: Long single and paired end reads will be given priority on the NextSeq.
* This month we are rolling out our newest library prep service – [[BioMicroCenter:Nextera|automated NexteraXT.]] Available in batches of 16 samples, prep includes quantification, library preparation, indexing, quality control and pooling.  
* '''November 1st''' we will be beginning our [https://mit-ki.ilabsolutions.com iLabs roll out.] On that day all walk up service calendars will be moved from openwetware and google calendar to iLabs. Please take the next few weeks to visit the lab and learn about the system.
* [[BioMicroCenter:PacBio|Pacific Biosciences]] will be presenting the Technology Seminar Series on '''October 22nd''' . We now provide PacBIo Service in the BioMicro Center using the RSII located at U.Mass Medical Center in Worcester.
* On this Friday, '''October 17th''', The BioMicro Center will be closed for a lab clean up. We will be making available consumables and equipment that are no longer useful for the core at 3PM. Please stop by and take anything useful before we dispose it.  


=== 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>


=== AUGUST 2014 ===
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>
We have set up a collaboration with the University of Massachusetts Medical Center Deep Sequencing Core Facility to provide Pacific Biosciences seqeucning to MIT users. We will be providing initial library preparation and quality control before sending the samples out to Worcester for sequencing. Completed sequence data will be returned through your BioMicro Center public folders. More details about PacBio sequencing can be found on our website.<BR><BR>
The Illumina pipeline has been upgraded to version 1.3. This upgrade includes quality control metrics for RNAseq and paired end reads as well as some changes under the hood to speed up data delivery. These quality control metrics are dependant on genome alignment, so will not be produced for samples aligned to phiX.<BR><BR>
Most of the price increases scheduled for the next fiscal year have been cancelled. We will be re-evaluating the rates in 6 month increments to ensure we remain within our mandated budget constraints.<BR><BR>
Our new co-op students, Austin Hendricks and Adam Perez have joined us and will be working in the Center through December.
The following packages have been added or updated on ROUS in the past few months:
* trinityrnaseq: r20140413p1
* bedtools: 2.20.1
* bowtie2: 2.2.3
* tophat: 2.0.12
* rsem: 1.2.15
* fastqc: 0.11.2
* bwa: 0.7.10
* pear: 0.9.4
* perl: 5.20.0
* samtools: 1.0
Older versions can still be selected using the module function.  We’ve also created a new mailing list rous_active_users@mit.edu to help keep folks who use Rous regularly up to date. You can sign up for it using Moira.


=== MAY 2014 ===
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.  
Some quick bullet pointed updates from BioMicro. We’re in the middle of rolling out several new initiatives right now that will hopefully be in the July newsletter.
* We are now offering sample prep using the [[BioMicroCenter:Nextera|Nextera XT]] system from Illumina. This modification of the Nextera uses only 1ng of input DNA (instead of the typical 50ng) and is significantly less expensive. Tuning it for insert size is somewhat more challenging than standard Nextera and so it should not be used where insert size is critical.
* [[BioMicroCenter:PricingFY2015|Pricing for 2015]] is up on our website. There is a link at the bottom of the pricing page.
* The Wafergen system is no longer available in the BioMicro Center. There is a system at Children’s Hospital if you absolutely need the Wafergen system. Most applications can also be done on the [[BioMicroCenter:RTPCR|Fluidigm BioMark]], which we still have in the lab.
* This month, we say goodbye to Scott Morin who will be leaving for medical school. Leigh Manley, who has transferred over from the Biopolymer core, will be taking over Illumina processing.
* Finally, the BioMicro Center will be shifting over to iLabs in the coming months. We are still early in the process but we would encourage everyone to [https://mit-ki.ilabsolutions.com/account/login register for iLabs] to help smooth the transition.


=== 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>


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>


=== MARCH 2014 ===
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>
A couple highlights of things going on in the center.
* We are resuming the [[BioMicroCenter:Technology_Seminar_Series|Technology Seminar Series]] this week with Roche speaking on Wednesday at lunch. The talk will focus on non-standard applications of the Light Cycler (SNP detection, etc).
* The Fraenkel lab has very kindly donated their [[BioMicroCenter:Covaris|Covaris sonicator]] to the core and we will be putting it under a service contract. We will need to put in place a small fee to cover the cost of the contract - likely starting in July. Training for new users will be available through [[BioMicroCetner:People|Shmulik]].
* We’ve generally had positive feedback about our new AA/BioA form and we’re expanding the new excel forms to include Illumina sequencing. [[BioMicroCenter:Forms|This new form will cover most types of sample preparation.]]
* Illumina is raising the prices on all of their sequencing reagents starting April 1. We lowered our prices very aggressively last year so, in order to break even, [[BioMicroCenter:Pricing#SEQUENCING|we will have adjust our prices slightly higher.]]
 
===  JANUARY, 2014 ===
I hope everyone had a fantastic holiday. We have several updates to let you know about. Since there are a few more than usual, I’m just going to give you the bullet list which you can check out on our website.
 
* Upgrade the [[BioMicroCenter:Software#BMC-BCC_Pipeline|basic analysis pipeline for Illumina]] – corrects some bugs, mostly with data overwrite problems, improves speed and provides more QC data, including GC bias checks on all HiSeq runs.
* New Co-op students -  [[BioMicroCenter:People|Ani Webb and Sam Kaplan]] started this week.
* New protocol for the Advanced Analytical allows us to do [[BioMicroCenter:Advanced_analytical_Fragment_analyzer|picoRNA]] samples on the machine. This cuts the cost of the analysis in half. We can still do the analysis on the BioAnalyzer if you prefer.
* If you run a lot of AA samples, you can lower your cost significantly by submitting the samples preloaded in a plate for the machine (contact us at biomicro@mit.edu if you are interested in this).
* Testing out a [[BioMicroCenter:Forms|new sample submission form]] based on Excel instead of Word. We’re piloting it with the BioAnalyzer form.
* We’re also trying to improve communication by sending database snapshots to users doing Illumina sequencing to make sure we have all the data entered correctly.
* Data storage costs have gone down significantly to [[BioMicroCenter:Pricing|$280/TB/y]]
* There are several IAP sessions highlighting software packages available from the MIT libraries. These include [ http://student.mit.edu/searchiap/iap-BD6D0CF8E096B284E0400312852F4A61.html Ingenuity Pathway Analysis,] [http://student.mit.edu/searchiap/iap-BD6D0CF8DC3DB284E0400312852F4A61.html GeneGO,] and our own [http://student.mit.edu/searchiap/iap-9289af8d41aa4e8e01425c9c633508c6.html training session on using Rous]
 
 


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]].




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== PUBLICATIONS ==
== PUBLICATIONS ==
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== PREVIOUS NEWSLETTERS ==
== PREVIOUS NEWSLETTERS ==
 
'''[[BioMicroCenter:News2015|2015]]'''<BR>
'''[[BioMicroCenter:News2014|2014]]'''<BR>
'''[[BioMicroCenter:News2014|2014]]'''<BR>
'''[[BioMicroCenter:News2013|2013]]'''<BR>
'''[[BioMicroCenter:News2013|2013]]'''<BR>

Revision as of 06:46, 20 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 role 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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18 April 2024

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N    18:40  3D Cell Culture - McLean Taggart, Emma Villares, Maximillian Marek, Scott LeBlanc, Adam Lyons and Jacob Belden‎ diffhist +24,060‎ CarterPaul talk contribs (Created page with "{{Template:CHEM-ENG590E}} ==Introduction== While most microfluidic devices incorporate a 2D cell culture design, in which a single layer of cells is grown on the bottom of a device, these systems suffer from poor <i>in vivo</i> mimicry, as, in the human body, most cells grow in all directions.<sup>https://doi.org/10.5114/aoms.2016.63743 1</sup> To address this limitation, 3D cell culture devices have been developed - in w...")
      18:38  CHEM-ENG590E:Wiki Textbook‎‎ 2 changes history +63‎ [CarterPaul‎ (2×)]
     
18:38 (cur | prev) +50‎ CarterPaul talk contribs (→‎Chapter 1 - Microfabrication)
     
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     18:36  3D Cell Culture - McLean Taggart, Emma Villares, Maximillian Marek, Scott LeBlanc, and Adam Lyons‎ diffhist +5,343‎ CarterPaul talk contribs (Added a Technique and applications section)
      10:20  Yarn Microfluidics - Roger Dirth‎‎ 11 changes history +406‎ [Rcostello‎ (11×)]
     
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10:17 (cur | prev) +38‎ Rcostello talk contribs (→‎Washburn Equation)
     
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