Ebola virus sequencing kit-list

Nanopore | amplicon | native barcoding

Document: ARTIC-EBOV-seqKit-v1.0.0
Creation Date: 2018-05-21
Revision Date: 2018-05-21
Forked from: doi:10.1038/nprot.2017.066
Author: Luke Meredith
Licence: Creative Commons Attribution 4.0 International License
Overview: The following protocol is adapted from the methods of Quick et al. (2017) Nature Protocols 12: 1261–1276 doi:10.1038/nprot.2017.066 and covers primers, amplicon preparation and clean-up, then uses a single-tube protocol to barcode and adaptor ligate the library, before running minION.
This document is part of the Ebola virus Nanopore sequencing protocol package:
http://artic.network/ebov/
Ebola primer scheme:
https://github.com/artic-network/primer-schemes/tree/master/ZaireEbola/V2
Ebola virus Nanopore sequencing protocol:
http://artic.network/ebov/ebov-seq-sop.html
Ebola virus Nanopore sequencing kit-list:
http://artic.network/ebov/ebov-seq-kit.html
Funded by the Wellcome Trust
Collaborators Award 206298/Z/17/Z --- ARTIC network

Library Preparation and Sequencing Reagents:

Product Supplier Cat No. Unit Cost # Req Cost  
Vilo SSIV RT Thermo 11756050 £793 1 £793  
Q5® Hot Start HF Polymerase (2xMM) NEB M0494L £611 1 £611  
NEBNext® UltraII™ End-prep NEB E7546L £722 1 £722  
Ebola Zaire V2 Primers* Thermo   £240 1 £220  
NEBNext® UltraII™ Ligation Module NEB E7595L £1,204 1 £1,204  
NEBNext® FFPE Repair Module NEB M6630L £539 1 £539  
Agencourt® AmpureXP™ Beads (60mL) FisherSci 10453438 £620 1 £620  
Ligation Sequencing Kit 1D Nanopore SQK-LSK108 £450 4 £1,800  
Low Input by PCR Barcoding Kit Nanopore SQK-LWB001 £500 2 £1,000  
Native Barcoding Expansion Kit Nanopore EXP-NBD103 £250 4 £1,000  
R9.4.1 flow cells Nanopore   £375 12 £4,500  
Qubit® dsDNA HS Assay Kit Thermo Q32851 £185 2 £370  
TOTAL COST         £13,379  

Equipment and Containment

Product Supplier Cat No. Unit Cost # Req Cost  
1000µL pipettes Gilson 10387322 £210 2 £420  
100µL pipettes Gilson 10442412 £210 2 £420  
10µL pipettes Gilson 10236072 £210 2 £420  
Sprout Microfuge (12V) PhilipHarris B8R04574 £170 2 £340  
PV-1 Mini Vortex WolfLabs PV-1 £150 2 £300  
Portable Heat Block Mobitec Pad3-H-CB £310 1 £310  
DynaMag-2 magnetic rack Thermo 12321D £540 1 £540  
MiniPCR™ Mini8 Cambio MPQP100001 £535 4 £2,140  
MyGo® Mini qPCR IT-IS SKU7642 £6,500 1 £6,500  
Qubit4® spectrophotometer Thermo Q33228 £2,578 1 £2,578  
Collapsible Tube racks (small x5) FisherSci 11770045 £50 1 £50  
Collapsible Tube racks (large x5) FisherSci 11710634 £50 1 £50  
Cold Racks (0.2-0.5mL) Sigma Z606634-1EA £50 2 £100  
Lab Mats StarLab E3860-0061 £25 2 £50  
USB Lights Amazon Jebsen-T05 £20 2 £40  
Portable UV Lamps Amazon B078LSR3MG £20 2 £40  
Portable glove box Amazon B01B1MGRR0 £70 2 £40  
TOTAL COST         £14,438  

Consumables and Disposables

Product (Number) Supplier Cat No. Unit Cost # Req Cost  
Stacked 1000µL Filter Tips (500) FisherSci 11977724 £70 2 £140  
Stacked 100µL Filter Tips (1000) FisherSci 11947724 £60 1 £60  
Stacked 10µL Filter Tips (1000) FisherSci 11907724 £60 1 £60  
1.5mL Eppendorf Tubes (500) StarLab I1415-5500 £20 2 £40  
0.6mL Eppendorf Tubes (500) StarLab I1405-1500 £20 1 £20  
0.2mL 8-strip tubes (1000) StarLab I1402-3600 £60 1 £60  
Qubit Reaction Tubes (500) Thermo Q32856 £50 1 £50  
MyGo PCR Tubes (500) IT-IS SKU7688 £85 1 £85  
BioBIn® Disposal Bins (100) FisherSci 10394373 £121 1 £121  
Gloves (Large, 100) StarLab SG-P-L £5 2 £10  
Gloves (Small, 100) StarLab SG-P-S £5 2 £10  
Paper Towels Generic     4 N/A  
Decon Wipes (240) MediPal PMC6038 £6 2 £12  
Back-tie Lab Gowns (45G) VWR 113-8316 £56 10 £56  
RNAse Away (250mL) Thermo 10328011 £60 2 £120  
DNA Away (250mL) Thermo 7010PK £20 2 £40  
TOTAL COST         £884  

Cold Chain, Power and Storage

Product (Number) Supplier Cat No. Unit Cost # Req Cost  
Flat dehydrated cold sheets (ThermaFreeze) Amazon B003ET2G74 £15 10 £150  
Thermos Radiance Cooler Bag Amazon B00BHW5B4U £10 4 £40  
Portable Fridge Bag Amazon B008N5UU3G £70 1 £70  
Credo Cube Series 20M 4L Pelican Contact Supp.     N/A  
PowerAdd Pilot Pro2 85Wh LiION 9-20V Amazon B013HXKZYW £80 2 £160  
Solar Charger, 85Wh, LiION 5-20V Amazon B00AE9FBCO £85 2 £170  
Goal Zero Yeti 150 Portable Power Station GoalZero SKU22004 £200 1 £200  
Goal Zero Nomad 28 Plus Solar Panel Goal Zero SKU11805 £250 1 £250  
Surge Protector Extension (4-plug) Belkin B0002AG0F2 £6 3 £18  
SKROSS Universal Mini Travel Adaptor Amazon B00OHSWG6C £10 2 £20  
Peli Air 1615 Waterproof Equipment Case R&S Comp. 121-8893 £550 1 £550  
Eagle Creek Cargo Hauler, 120L Amazon B01HIGO3OC £150 1 £150  
BESTEK 200W Power Inverter DC 12V Amazon B01N2P9V64 £30 1 £30  
Samsung Portable SSD T5 1TB Amazon B074M774TW £320 2 £640  
Seagate® 5TB External HD Amazon B01M058Q39 £119 2 £238  
TOTAL COST         £2,686