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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 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 ( 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.


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 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.


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"


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