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{{BioMicroCenter}}
{{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.  
The MIT BioMicro Center has two PromethION P2 Solos, each capable of running two concurrent flowcells. The Center supports all current standard ONT library prep protocols including both ligation and tagmentation methods as well as direct RNA measurement. Run protocols such as adaptive sampling are available. Each flowcell is run to completion and not reused - prices are for full flowcells.
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==Oxford Nanopore Sequencing==
==Oxford Nanopore Sequencing==
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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.   
A variety of preparation kits allow DNA 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.   
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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.
Nanopore library contains adaptor with both motor protein and tether. If tether interacts with a nanopore successfully, the motor protein will shift the molecule into and through the protein nanopore. The voltage set across the nanopore shifts 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 and/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.
Contaminants known to cause issues for the nanopores even at low amounts include:  
*EDTA
*Alcohols (EtOH, iPrOH
*High concentrations of salts (NaCl, guanidinium chloride,guanidinium isothiocyanate
*phenol
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Modified basecalling is available on request. Not all desired basecalled modifications are possible in a single sequencing run with the current chemistries and basecalling software, but trace data (fast5) can be taken and re-basecalled using different basecallers. Re-basecalling can be done as a separate bioinformatic project.
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For adaptive sampling, the user must provide at least a FASTA genome file and, optionally a BED file with the region(s) of interest. It is important that for both enrichment and depletion such region(s) only entail 0.1-10% of expected reads
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[[Image:Nanopore.jpg|300px|middle]]
[[Image:Nanopore.jpg|300px|middle|Ji, CM et al (2024). Viruses, 16(5), 798.]] <br><br>
[[Image:Spanreads.jpg|200px|middle|Page Lab assembled ultra long read gDNA data showing a long read spanning Illumina contigs]] <br><br>
[[Image:IGV_vimentin.jpg|300px|middle|IGV spanning the Vimentin gene with assembled amplified cDNA]]
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  |[[Image:PromethION.jpg|center|200px]]© Oxford Nanopore Technologies
  |[[Image:PromethION.jpg|center|200px]]© Oxford Nanopore Technologies
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  | '''AVG READS/FLOWCELL'''<BR>  
  | '''AVG OUTPUT/FLOWCELL'''<BR>  
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  | 50 Gb (highly variable)
50 Gb
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  |-
  |'''MAX TIME/FLOWCELL'''
  |'''MAX TIME/FLOWCELL'''
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  | 3 days (adjustable)
3 days (adjustable)
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|'''BEST FOR'''
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*LONGEST READS
*COUNTING APPLICATIONS
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Latest revision as of 12:29, 18 July 2025

HOME -- SEQUENCING -- LIBRARY PREP -- HIGH-THROUGHPUT -- COMPUTING -- OTHER TECHNOLOGY

The MIT BioMicro Center has two PromethION P2 Solos, each capable of running two concurrent flowcells. The Center supports all current standard ONT library prep protocols including both ligation and tagmentation methods as well as direct RNA measurement. Run protocols such as adaptive sampling are available. Each flowcell is run to completion and not reused - prices are for full flowcells.

Oxford Nanopore Sequencing[edit]

Service Nanopore Sequencing
INPUT Nanopore libraries
MIN CONCENTRATION Dependent on library type, read count not guaranteed
INCLUDED SERVICES
  • Quality Control:UV-vis measurement
  • Nanopore Sequencing
  • Demultiplexing
ADDITIONAL SERVICES
  • Quality Control
  • Nanopore library preparation
  • Modified basecalling available on request
  • Reference FASTA genome and BED regions file required for adaptive sampling
DATA FORMATS
  • FASTQ (stored 90 d and archived)
  • FAST5 (stored 30 d and deleted)
  • Assorted Nanopore QC documents
PRICING NANOPORE LIBRARIES and NANOPORE SEQUENCING
SUBMISSION

A variety of preparation kits allow DNA 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.

Nanopore library contains adaptor with both motor protein and tether. If tether interacts with a nanopore successfully, the motor protein will shift the molecule into and through the protein nanopore. The voltage set across the nanopore shifts 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 and/or fastq.

Contaminants known to cause issues for the nanopores even at low amounts include:

  • EDTA
  • Alcohols (EtOH, iPrOH
  • High concentrations of salts (NaCl, guanidinium chloride,guanidinium isothiocyanate
  • phenol



Modified basecalling is available on request. Not all desired basecalled modifications are possible in a single sequencing run with the current chemistries and basecalling software, but trace data (fast5) can be taken and re-basecalled using different basecallers. Re-basecalling can be done as a separate bioinformatic project.

For adaptive sampling, the user must provide at least a FASTA genome file and, optionally a BED file with the region(s) of interest. It is important that for both enrichment and depletion such region(s) only entail 0.1-10% of expected reads

Ji, CM et al (2024). Viruses, 16(5), 798.

Page Lab assembled ultra long read gDNA data showing a long read spanning Illumina contigs

IGV spanning the Vimentin gene with assembled amplified cDNA

Oxford Nanopore Sequencer[edit]

SPEC PromethiON P2 Solo
SEQUENCER
© Oxford Nanopore Technologies
AVG OUTPUT/FLOWCELL
 50 Gb (highly variable)
MAX TIME/FLOWCELL 3 days (adjustable)
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