BioMicroCenter:QC

The BioMicro Center hosts several instruments to assist in quantifying nucleic acids and determining their size and purity. All samples submitted to the BioMicro Center for assisted services are routinely assayed on these instruments and they are used to monitor success of library production steps. Quality control is also a stand alone service available to researchers. Quality control instruments are currently located in 68-322.

Visual for determining which DNA sizing instrument best suits the sample.

Instrument	Description	Measures	Type
AATI Fragment Analyzer	Capillary Electrophoresis	Size, Quantity	Request via iLabs
AATI FemtoPulse	Capillary Electrophoresis	Size, Quantity	Request via iLabs
Agilent BioAnalyzer	Microfluidics	Size, Quantity	Schedule via iLabs
Nanodrop	Absorbance	Purity, Quantity	Walk-up
Varioskan:Picogreen	Absorbance	Quantity	Schedule via iLabs

AATI FRAGMENT ANALYZER

Service AATI FRAGMENT ANALYZER INPUT 5uL for standard 2uL/well for preload SUBMISSION MIT - ilabs External - form Preloaded rows must be in semiskirted plates from the BioMicro Center (or equivalent). UNIT Samples or preloaded rows TURN AROUND Typically < 1 business day SAMPLE SUBMISSION 9a-4:30p normal weekdays. Samples brought by after 4:30p must be accompanied by cookies. DONATED BY Department of Biology	The Advanced Analytical Fragment Analyzer (FA) is a highly efficient and accurate fluorescence-based electrophoresis instrument used to size and quantify DNA and RNA. It is faster and more cost effective than the BioAnalyzer2100, and can handle unsupervised runs of up to 192 samples. Each run takes ~60 minutes and 2 μL of sample. Users may submit any volume of sample with the expectation that if there is less than 2 μL, the samples will be diluted. To save money and submit a larger quantity of samples, users may come into the BMC and obtain a special 96 well plate or plates. For mass submission, 2 μL must be put into each sample well row by row. There is a way to submit rows in iLabs, but please remember to come and get special plates from the BMC to do mass submission. The Fragment analyzer was purchased in 2012 and upgraded to handle 48 samples in a batch in 2017. Fragment analyzer reports a "RIN eQuivalent Number (RQN) instead of RIN.
Assay Sizing Range Concentration Range High Sensitivity DNA 50bp - 5kbp Fragment: 5pg-1ng/uL Smear: 50pg-5ng/uL Nano RNA 50bp - 5kbp Pico RNA (recommend FemtoPulse instead) 50bp - 5kbp 50pg-5ng/uL

AATI FEMTO PULSE

Service AATI FEMTO PULSE INPUT 5uL for standard 2uL/well for preload SUBMISSION MIT - ilabs -- External - form Preloaded rows must be in semiskirted plates from the BioMicro Center (or equivalent). UNIT Samples or preloaded rows TURN AROUND Typically < 1 business day DONATED BY MIT CEHS	The FEMTO Pulse (FP) is an instrument that provides a remarkable upgrade over the existing FA and Agilent BioAnalyzer2100 technologies that have been available for many years. While still an instrument to analyze the lengths of nucleic acids, the FEMTO Pulse adds a pulse filed generator to allow the separation and characterization of significantly longer molecules, out to 200,000 base pairs. Additionally, the FP has significantly improved optics that allow approximately two orders of magnitude of additional sensitivity. Where the FA bottoms out a sensitivity of 2-3pg/ul, the FP has nearly 100x improved sensitivity which may enable this instrument to directly observe molecular reactions without the need for amplification or modification with radioactive nucleotides. The FEMTO Pulse runs 12 samples at a time using 2ul of material. Each run takes ~90 minutes to run. It is *not* a replacement for the Fragment Analyzer and is optimized for very low inputs or very long samples.
Assay Sizing Range Concentration Range NGS DNA 50bp - 5kbp Smear: 2.5-500pg/uL Fragment 50fg-5pg/uL Genomic DNA 2kbp - 160kbp Smear: 2.5 - 500pg/uL Femto RNA 50bp - 5kbp 2.5pg-500pg/uL

AGILENT BIOANALYZER 2100

Service Agilent BioAnalyzer SERVICE WALKUP INPUT 1uL/well SCHEDULE MIT iLabs UNIT Per Chip RUN TIME ~1 hour	The Agilent 2100 BioAnalyzer is a microfluidics device that performs size determination and quantification of small samples of DNA, RNA, or Protein. In addition, the BioAnalyzer is able to perform flow cytometry on small numbers of cells. Samples can be run on the BioAnalyzer by individual users; the BioMicro Center does not currently accept sample submissions to be run on the BioAnalyzer by BMC staff. Samples can be run by individual users on the BioAnalyzer after a user has received training by emailing bmcwetlab@mit.edu (Core Labs only please). This service will be discontinued if we find the machine is abused. Once you are trained in the use of the BioAnalyzer you are welcome to sign up for usage on ilabs.
Assay Sizing Range Concentration Range High Sensitivity DNA 50bp - 7kbp 5-500pg/ul RNA Nano 25bp - 5kbp 25-500 ng/ul total RNA RNA Pico 25bp - 5kbp 0.05-5 ng/ul total RNA small RNA 6bp-150bp 0.05-2 ng/ul smallRNAs High Sensitivity Protein 10kD-250kD 0.3ng/ul Note: not all assays are listed.

NanoDrop ND-1000

Instrument NANODROP TYPE WALKUP PRICING NO CHARGE WAVELENGTH 220-750nm MIN CONC ~10ng/uL SIGNUP No Signup Necessary.

The NanoDrop ND-1000 is a full-spectrum (220 - 750nm) spectrophotometer that measures 1ul samples without the use of cuvettes or the need for dilution. The NanoDrop ND-1000 is located at the BMC, building 68-322 and is FREE for core department use