Editing BioMicroCenter:QC

{{BioMicroCenter}}

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.
[[Image:FA_vs_FP.jpeg|thumb|right|400px|Visual for determining which DNA sizing instrument best suits the sample.]]
{|class="wikitable" border=1
 ! Instrument
 ! Description
 ! Measures
 ! Type
 |-
 | [[BioMicroCenter:QC#AATI_FRAGMENT_ANALYZER|AATI Fragment Analyzer]]
 | Capillary Electrophoresis
 | Size, Quantity
 | Request via iLabs
 |-
 | [[BioMicroCenter:QC#AATI_FEMTO_PULSE|AATI FemtoPulse]]
 | Capillary Electrophoresis
 | Size, Quantity
 | Request via iLabs
 |-
 | [[BioMicroCenter:QC#AGILENT_BIOANALYZER_2100|Agilent BioAnalyzer]]
 | Microfluidics
 | Size, Quantity
 | Schedule via iLabs
 |-
 | [[BioMicroCenter:QC#NanoDrop_ND-1000|Nanodrop]]
 | Absorbance
 | Purity, Quantity
 | Walk-up
 |-
 | [[BioMicroCenter:Varioskan|Varioskan:Picogreen]]
 | Absorbance
 | Quantity
 | Schedule via iLabs
 |-
 | [[BioMicroCenter:Varioskan|Varioskan:Synergy_H1]]
 | Absorbance
 | Quantity, Purity
 | Schedule via iLabs
|}

== AATI FRAGMENT ANALYZER ==
{|
 |- style="vertical-align: top;"
 |style="width: 400px;"|
 {| class="wikitable" border=1
  !Service 
  !AATI FRAGMENT ANALYZER
  |-
  |INPUT || 5uL for standard <br> 2uL/well for preload
  |-
  |SUBMISSION || MIT - [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=4110 ilabs] <BR> External - [[BioMicroCenter:Forms|form]] <BR> 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. <BR> Samples brought by after 4:30p must be accompanied by cookies.
  |-
  |DONATED BY || Department of Biology
 |}
 |
The [[BioMicroCenter:Advanced_analytical_Fragment_analyzer|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. <BR><BR>

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.
 |
[[Image:FA.jpg|right]]
 |- 
 |colspan = "2"|
 {| class="wikitable" border=1
  ! Assay
  ! Sizing Range
  ! Concentration Range
  |-
  |High Sensitivity DNA
  |50bp - 5kbp
  |Fragment: 5pg-1ng/uL <br> Smear: 50pg-5ng/uL
  |-
  |Nano RNA
  |50bp - 5kbp
  |
  |-
  |Pico RNA (recommend FemtoPulse instead)
  |50bp - 5kbp
  |50pg-5ng/uL
  |}
 | 
|}

== AATI FEMTO PULSE ==
{|
 |- style="vertical-align: top;"
 |style="width: 400px;"|
 {| class="wikitable" border=1
  !Service 
  !AATI FEMTO PULSE
  |-
  |INPUT || 5uL for standard <br> 2uL/well for preload
  |-
  |SUBMISSION || MIT - [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=4110 ilabs] -- External - [[BioMicroCenter:Forms|form]] <BR> 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 [[BioMicroCenter:FemtoPulse|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. <BR><BR>

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.  <BR><BR>
 |
[[image:BMC_FP_instrument.jpeg|right]]
 |- 
 |colspan = "2"|
 {| class="wikitable" border=1
  ! Assay
  ! Sizing Range
  ! Concentration Range
  |-
  |NGS DNA
  |50bp - 5kbp
  |Smear: 2.5-500pg/uL <br> Fragment 50fg-5pg/uL
  |-
  |Genomic DNA
  |2kbp - 160kbp
  |Smear: 2.5 - 500pg/uL
  |-
  |Femto RNA 
  |50bp - 5kbp
  |2.5pg-500pg/uL
  |}
 | 
|}

== AGILENT BIOANALYZER 2100 ==
{|
 |- style="vertical-align: top;"
 |style="width: 300px;"|
 {| class="wikitable" border=1
  !Service 
  !Agilent BioAnalyzer
  |-
  |SERVICE || WALKUP
  |-
  |INPUT || 1uL/well
  |-
  |SCHEDULE || [https://mit.ilabsolutions.com/equipment/show/265040 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. <BR><BR>

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.
 |
[[Image:Presentation4.jpg|right|200px]]
 |-
 |colspan="2"|
 {| class="wikitable" border=1
  ! 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 == 
{| align=left 
 |- style="vertical-align: top;"
 |style="width: 300px;"|
 {| class="wikitable" border=1
  ! 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 [[BioMicroCenter:CoreDeps|core department]] use
 |
[[Image:Nd-1000.jpg|right|200px]]
|}