Editing BioMicroCenter:Oxford Nanopore Technologies

{{BioMicroCenter}}
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The MIT BioMicro Center has two PromethION P2 Solos. We support de novo sequencing and have tested some RNA-seq metrics on these platforms. Each flowcell can potentially accommodate many barcoded samples (depending on sample quality and desired coverage) and each unit can theoretically run up to 2 flowcells simultaneously depending on the projects. 
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==Oxford Nanopore Sequencing==
{|
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  !Service 
  !Nanopore Sequencing
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  |INPUT || Nanopore libraries
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  |MIN CONCENTRATION || Dependent on library type, read count not guaranteed
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  |INCLUDED SERVICES 
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* Quality Control:UV-vis measurement
* Nanopore Sequencing 
* Demultiplexing
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  |ADDITIONAL SERVICES ||
* Quality Control
* [[BioMicroCenter:NanoPore_Library_Prep|Nanopore library preparation]]
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  |DATA FORMATS 
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*FASTQ (stored 90 d and archived) 
*FAST5 (stored 30 d and deleted) 
*Assorted Nanopore QC documents
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  |PRICING || [[BioMicroCenter:Pricing#LONG_READ_LIBRARIES|NANOPORE LIBRARIES]] and [[BioMicroCenter:Pricing#LONG_READ_SEQUENCING|NANOPORE SEQUENCING]] 
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  |SUBMISSION 
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* MIT - [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=3863 ilabs] 
* External - [[BioMicroCenter:Forms|form]]
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A variety of preparation kits allow DNA, cDNA, or direct RNA to be sequenced.  The input amount necessary for each type of sample varies according to the desired result.  For the longest reads of genomic DNA, micrograms worth of clean starting material provide the highest quality of data, but not the highest amounts of reads.  For amplicons including cDNA made from RNA, amplifying hundreds of nanograms should be simple, thus a lower input in the picograms should be reasonable.  
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During library preparation, adaptor consisting of motor protein and tether is ligated to the ends of RNA or DNA with tether furthest from the template.  Adaptors can also be bought with barcodes for multiplexing.  If tether interacts with a nanopore successfully, motor protein will shift the molecule into and through the protein nanopore.  A voltage is set across the nanopore and the current will shift as base pairs move through the pore. Nanopores are arranged in an array such that multiple molecules can be sequenced simultaneously.  Sequencing and demultiplexing all occur in real time providing fast5 or fastq.
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Contaminants known to cause issues for the nanopores so far include: EDTA, ethanol, isopropanol, NaCl, guanidinium chloride, guanidinium isothiocyanate, and phenol. The nanopores on the flowcell can be directly affected by low amounts of contamination.  
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[[Image:Nanopore.jpg|300px|middle]]
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==Oxford Nanopore Sequencers==
{| class="wikitable" border=1 
 !width=100| SPEC
 !width=250| PromethiON P2 Solo
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 |'''SEQUENCER'''
 |[[Image:PromethION.jpg|center|200px]]© Oxford Nanopore Technologies
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 | '''AVG READS/FLOWCELL'''<BR> 
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50 Gb
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 |'''MAX TIME/FLOWCELL'''
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3 days (adjustable)
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 |'''BEST FOR'''
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*LONGEST READS
*COUNTING APPLICATIONS
|}