NANOPORE SEQUENCING

TURNAROUND TIme:

Nanopore runs start every Monday through Friday at 2PM, with results returned within 24 hours!

OUR SERVICE:

WE SEQUENCE PLASMIDS, AMPLICONS, PHAGES, BACMIDS, AND COLONY PICKS TOO!

Also included in the bioinformatics processing pipeline is an alignment with your preferred reference sequence (FASTA format) - if desired. Just provide the sequence (or accession number) and we will return the alignment to you along with original read data.

sample submission deadlines

2PM Mon - Friday for purified plasmids, amplicons, phages and bacmids.

10AM Mon - Friday for colony picks and/or samples that require RCA (rolling circle amplification). Please contact us at dnaseq@berkeley.edu prior to submitting colony picks for Nanopore sequencing. The earlier you get us your colony picks the better!

LIBRARY KITS WE USE / OFFER:

A RAPID BARCODING KIT: This is our primary method, with a ~24 hour turnaround. It is a transposase-based (random) tagmentation barcoding protocol for maximum efficiency and speed.

NATIVE BARCODING KIT: A ligation-based barcoding approach for those requiring more control over read length. PLEASE call or email before you request/submit samples for native barcoding. The cost is slightly higher, it requires more bench time, and therefore has a longer turnaround (2-3 days).

DNA quantification guideline:

We no longer require dna quantification prior to nanopore sequencing!

However - if you have the ability to assess the DNA concentration (and quality), it is always appreciated if you can provide that information on the request form accompanying your sample(s).

We highly recommend using a Qubit assay or the Promega Quantifluor dsDNA System to measure your DNA concentration (no Nanodrop measurements please).

service rates:

For Rapid Barcoding Kit - $15/sample

For Ligation Barcoding Kit - $60/sample

LBNL and CHORI, add 10%

Off-campus, add 61%

Pricing includes pre-treatment of plasmids, library prep, Nanopore run, and basic bioinformatics

SAMPLE SUBMISSION GUIDELINES:

All samples should be in water or TE.

How much DNA to submit for Rapid and Native Barcording:

Colony picks ~10ul
Purified plasmids 20ul at 50ng/ul or more
Amplicons 20ul at 50ng/ul or more
Bacmids 20ul at 100ng/ul or more

Please email your plasmid sequences in FASTA format for reference mapping if available.

Sample names:

Letters, Numbers, and "_" only.

Please do not use SPACES (e.g., " ") or other unusual characters.

Please use short names if at all possible.

HOW TO PLACE ORDERS:

🧬 Submit 20ul of >50ng/ul plasmids and amplicons in 1.5 ml Eppendorf tubes or a 96well plate

🧬 Please label the top of the tube with a permanent marker as clearly as possible with alpha-numeric characters only

🧬 Bring your samples to 310 Barker Hall or ship via FedEx

🧬 Fill out and email Full Plasmid Sequencing order form or Full Plasmid Sequencing-Plate order form to dnaseq@berkeley.edu. · · · Please include a printed form along with your samples

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