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Protocols

SpotOn specifications

Information


Unique identifier OMICS_21623
Name SpotOn
Software type Application/Script
Interface Web user interface
Restrictions to use None
Input data A 3D structure of the protein-protein complex.
Input format PDB
Computer skills Basic
Stability Stable
Registration required Yes
Maintained Yes

Maintainers


  • person_outline Alexandre M.J.J. Bonvin
  • person_outline Irina Moreira

Publication for SpotOn

SpotOn citations

 (32)
library_books

MEGAN LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs

2018
Biol Direct
PMCID: 5910613
PMID: 29678199
DOI: 10.1186/s13062-018-0208-7

[…] Sequencing Kit SQK-LSK108 (Oxford Nanopore Technologies, Oxford, UK) for 1D sequencing according to the manufacturer protocol. Sequencing was performed using an early access MinION device (ONT) on a SpotON FLO-MIN106 flowcell (R9.4). The run was stopped after 22 h due to low number of active pores. Fast5 files were obtained with MinKNOW (v1.3.30, ONT) using a 48 h genomic sequencing protocol. Bas […]

call_split

Complete Genome Sequence of the Methanococcus maripaludis Type Strain JJ (DSM 2067), a Model for Selenoprotein Synthesis in Archaea

2018
Genome Announc
PMCID: 5887029
PMID: 29622618
DOI: 10.1128/genomeA.00237-18
call_split See protocol

[…] ophoresis. Extracted DNA was prepared following the protocol for 1D2 (SQK-LSK308) sequencing of genomic DNA without any size selection. Sequencing was performed with a MinION device (MinION Mk1B) and SpotON flow cell Mk I (R9.5) using MinKNOWN version 1.10.11 as recommended by the manufacturer (Oxford Nanopore, Oxford, UK). Base calling of the raw data was performed using Albacore version 2.0.1. I […]

library_books

Real time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building

2018
GigaScience
PMCID: 5905381
PMID: 29617771
DOI: 10.1093/gigascience/giy033

[…] (ONT) and nuclease-free water. Then 12 µL of the amplicon library was diluted in 75 μL of running buffer with 35 µL RBF, 25.5 uL LLB, and 2.5 μL nuclease-free water and added to the flow cell via the SpotON sample port. The NC_48Hr_sequencing_FLO-MIN107_SQK-LSK108_plus_Basecaller.py protocol was initiated using the MinION control software, MinKNOW (offline version provided by ONT). […]

library_books

Identification of potential regulatory mutations using multi omics analysis and haplotyping of lung adenocarcinoma cell lines

2018
Sci Rep
PMCID: 5862974
PMID: 29563587
DOI: 10.1038/s41598-018-23342-1

[…] it SQK-LSK208 for 2D, SQK-LSK108 for 1D and SQK-LSK308 for 1D2. Libraries were then purified using MyOne C1 beads (65001, Thermo Fisher Scientific) and sequenced for 48 hours by MinION Mk 1B with the SpotON Flow Cell (FLO-MIN106, R9.4 version for 2D; FLO-MIN107, R9.5 version for 1D and 1D2, Oxford Nanopore Technologies).FASTQ files were generated from the FAST5 files using poretools. Sequences wer […]

library_books

Heating and Cooling Rates With an Esophageal Heat Exchange System

2018
PMCID: 5882296
PMID: 29283916
DOI: 10.1213/ANE.0000000000002691

[…] ia, are likely to be artifactually warmed or cooled by the test heat exchange system. We therefore estimated core temperature with a zero-heat-flux forehead monitor (Bair Hugger Thermometer, formerly SpotOn [3M; St. Paul, MN]). Ambient and core temperatures, end-tidal sevoflurane, mean arterial pressure, and heart rate were measured at 10-minute intervals during warming and cooling.During each hea […]

library_books

Quantifying the stability of oxidatively damaged DNA by single molecule DNA stretching

2018
Nucleic Acids Res
PMCID: 5934642
PMID: 29522114
DOI: 10.1093/nar/gky148

[…] abs) (the 5.0 μm bead is shown in the figure). The flow cell is moved at a fixed loading rate of 10 pN/s, in ∼4 nm steps (nPoint), and increasing DNA tension is recorded by a lateral effect detector (SpotOn, Melles Griot). Though this instrument is capable of varying loading rates, faster rates compromise the signal-to-noise, while slower rates reveal drift in the micropipette position. Instrument […]

Citations

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SpotOn institution(s)
CNC - Center for Neuroscience and Cell Biology, FMUC, Universidade de Coimbra, Coimbra, Portugal; Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, The Netherlands; Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Bobadela, Portugal; Department of Genetics and Genomics and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; CMUP/FCUP, Centro de Matemática da Universidade do Porto, Faculdade de Ciências, Rua do Campo Alegre, Porto, Portugal

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