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Cornell University

PacBio Sequencing

We are happy to offer long-read sequencing utilizing the PacBio Revio system! These sequencing runs are sent out to external providers but supported by the Genomics Facility (including local ordering/sample drop-off, QC checks and data management/distribution/archive), and without the need to acquire a quote/PO outside Cornell. The PacBio Revio system is a high-throughput long-read sequencing platform that utilizes Single Molecule, Real-Time (SMRT) sequencing technology and SPRQ HiFi chemistry.  The SMRT Cell 25M typically generates ~ 15-20M raw reads, yielding up to 90-100 Gbp of HiFi data, although exact outputs may vary with sample. HiFi reads combine long fragment lengths with very high per-base accuracy — reads up to about 30 kb long with greater than 99.9% accuracy are possible as each DNA molecule is sequenced repeatedly in a circular consensus process (CCS) that averages out errors. 

Currently we support PCR-free whole-genome sequencing (WGS) and full-length RNA sequencing on the PacBio Revio platform. 

  • WGS: please submit at least 3ug of high molecular weight DNA in 50uL (minimum 60ng/ul). Genomic DNA sample quality should be assessed on the Femto Fragment Analyzer to confirm the size distribution prior to library prep and sequencing. To include the gDNA QC check with the sequencing order, please prepare a separate aliquot with concentration ≤ 0.5 ng/ul in minimum 5ul volume.
  • Full-length RNA sequencing: please submit a minimum of 1ug total RNA in 25ul (minimum 40ng/ul). RNA integrity should be assessed prior to library prep and sequencing, with RIN/RQN value >7.0. To include the RNA QC check with the sequencing order, please prepare a separate aliquot with concentration ≤ 5ng/ul in minimum 5ul volume. 

Sample Preparation Guidelines:

ApplicationSample TypeSpecification
Whole GenomeTissue 60mg fresh or frozen tissue
Blood1mL - Please provide in K2 EDTA tubes
HMW DNA> 3µg HWM DNA (per Gb genome size); Volume: 50µl; GQN >7.0 for 30kb
RNA SequencingTissue 60 mg of fresh or frozen tissue, 20 mg of stabilized tissue
Cells>Recommended: 1e+6 cells frozen and pelleted 
Total RNA> 1 µg Total RNA; Volume: 25µl; RIN: >7.0
PureTargetDNA inputTotal 16µg (e.g., 2µg per sample if 8 samples. 4µg per sample if 4 samples)
AmpliconDNA input1-3Kb (>200ng); 3-5Kb (>400ng), 5-10Kb (>500ng), >10Kb (>700ng); Volume: 25µl of column purified amplicons

 

Library typeLibrary sizeMinimum Amount required per SMRT cell (ng)*
Volume requirement: 25µl
WGS10Kb120ng
15Kb180ng
18Kb210ng
21Kb250ng
Amplicon<3Kb75ng
3-10Kb100ng
>10Kb120ng
Iso-Seq<3Kb75ng
3-10Kb100ng
Kinnex Single cell RNA14-15Kb125ng
Kinnex Single cell RNA16-17Kb125ng
Kinnex 16s18-19Kb125ng
AAV2.1-2.6Kb100ng