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Pacific Biosciences Core Enterprise

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    The Core operates a Pacific Biosciences Sequel II Instrument with the newest version of the run chemistry (read lengths over 50kb) and SMRTlink data analysis. The service includes (as a package deal): library construction from submitted DNA or RNA, sequencing of one SMRTcell, and quality filtering/run metrics. Multiplexing is available using either internal PacBio Barcoded Universal Primers (for amplicon libraries) or PacBio Barcoded Adapters. Additional bioinformatics options are available for a fee. Please contact us about your project. We'd love to work with you!

Introduction/Basics
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Services
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  • Our package deal includes library building and sequencing of one SMRTcell.
  • Additional SMRTcells can be added at a discounted price.
  • Multiplexed library builds are available. The options for this are: barcodes internal to your amplicon(s) (you would have to add these during amplification using PacBio's Barcoded Universal Primers) or barcodes in the PacBio SMRTbell adapters (added by the Core during library prep).
  • Bioinformatics services offered include consensus (Read Of Insert) analysis, IsoSeq analysis, assembly, mapping, variant, motif, and/or base modification detection options.
  • Data delivery options for non-UMass customers are to have the data uploaded to an outside server (using SFTP) or transferred to an external drive meeting our security/speed requirements and shipped overnight.
  • Material may be turned in as RNA or DNA.SMRTbell Template
Library Types:
Amplicon or short fragment
IsoSeq / cDNA
(from total RNA)
Genomic or plasmid DNA
(includes shearing step)
HiFi Genomic
(tightly sized for <2Gb genomes)
Indexed (for multiple lib. types)
Imaging Times:
10 hours
(amplicons and 16S)
15 hours
(de novo and structural variants)
24 hours
(IsoSeq libraries)
30 hours
(by special request for HiFi and metagenomics)

Tools
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Drop-off locations:
Samples can be left in the labeled fridges at these locations
for 11:00 AM pickup each business day:
Biotech2 outside Suite 207
LRB 6th floor mailroom
ASC8-2058 mailroom
We are also available by appointment if you need to visit with us.
Our shipping address for off-campus customers is
Rose-Gordon Bldg. Rm. 141, 222 Maple Ave, Shrewsbury, MA, 01545.

Publications
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The PacBio Core Enterprise would be pleased to have you mention us in the acknowledgements section of any publications or presentations of data generated with our support.
If you would like to have your publication listed on the Core's website to help highlight the work UMass researchers are doing, email us the reference at PacBio@umassmed.edu.

A collection of papers highlighting applications possible with PacBio technology
https://www.mdpi.com/journal/genes/special_issues/SMRT_sequencing#info

Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads
https://www.ncbi.nlm.nih.gov/pubmed/31711268/

RADAR-seq: A RAre DAmage and Repair sequencing method for detecting DNA damage on a genome-wide scale
https://www.ncbi.nlm.nih.gov/pubmed/31247470/

The Origin of the Haitian Cholera Outbreak Strain
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030187/

Direct Detection and Sequencing of Damaged DNA Bases
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3264494/

Direct Detection of DNA Methylation During Single-Molecule, Real-Time Sequencing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879396/

Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287169/

Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia
http://www.ncbi.nlm.nih.gov/pubmed/22504184/

Going beyond five bases in DNA Sequencing
http://www.ncbi.nlm.nih.gov/pubmed/22575758

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