MBCL IDT Portal
PBCE Services
Library Prep and Sequencing
- Our package deal includes library construction, sequencing of one SMRTcell, quality filtering, and delivery of data and run metrics.
- Additional SMRTcells can be added at a discounted price.
- Size-selection of large fragments on the Sage Science Blue Pippin pulsed-field electrophoresis system is available separately or bundled as part of certain library prep packages.
- 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)
- Barcodes in the PacBio SMRTbell adapters (added by the Core during library prep).
- Material may be turned in as RNA or DNA. If you are off-campus, PacBio has some recommended guidelines for sample shipping.
Bioinformatics
- Bioinformatics services offered include:
- Read Of Insert (ROI) analysis aka Circular Consensus Sequencing (CCS)
- Demultiplexing
- ssAAV demultiplexing and analysis
- IsoSeq analysis
- Kinnex (MAS-Seq) analysis
- Assembly, scaffold, or hybrid assembly
- Mapping to a genome or transcriptome
- Variant, motif, and/or base modification detection options
- The recommended data delivery option is to have the data uploaded to Globus. You do not need a full Globus subscription to receive data, however you do need a registered email account. Information about Globus subscription and personal use is available at https://app.globus.org.
| Library Types: |
|---|
| Amplicon or short fragment |
| AAV fragments (range of sizes, possibly single-stranded) |
| IsoSeq / cDNA (from total RNA) |
| Genomic or plasmid DNA (includes shearing step) |
| HiFi Genomic (tightly sized for <2Gb genomes) |
| Kinnex (MAS-Seq) single-cell (from cDNA with 3' or 5' 10X kit) |
| optional add-on: Indexed (for any library type) |
| Imaging Times: |
|---|
| 10 hours (recommended for short amplicons and 16S) |
| 15 hours (microbial de novo and structural variants) |
| 20 hours (by special request) |
| 24 hours (AAV and IsoSeq libraries) |
| 30 hours (Kinnex, HiFi, metagenomics, de novo low input) |
Pricing and Payment Policy
Please email PacBio@umassmed.edu to get a quote for your desired services.
Processing and analyzing a sample requires time and reagents. Payment for services is the responsibility of the user submitting the sample and should be rendered in a timely fashion. In the event of a reagent or equipment failure, samples will be rerun at the next possible opportunity with no additional charge.
Clients withdrawing samples prior to the analysis run will be charged a fee to recover QC assay costs. For the return of archived post-analysis samples, clients will be charged a delivery fee per sample.
A signed ticket or email authorization indicates that the holder of the listed account consents to payment in accordance with this policy.
Inclement Weather Policy
In case of extreme weather or campus closures, the machines will be operating but we may not conduct a sample pickup. Please email us to arrange for sample drop-off if the weather is questionable. The PBCE, DSCL, & MBCL are closed when UMass Chan is on "inclement weather alert".
MBCL IDT Portal