SeqCenter will be closed Monday, January 20th, 2025 in observance of Martin Luther King Jr. Day. We will be unable to receive packages on this day. Two-week turnarounds will be offset by 1 day for this closure.

PacBio AAV

PacBio WGS PacBio AAV PacBio IsoSeq

We are proud to be a PacBio-sponsored adeno-associated virus (AAV) sequencing facility and to take part in this growing field where accuracy is key to the development of new therapeutics. PacBio’s SMRT platform with CCS is ideal for identifying mutations, truncations, and host integration events in AAV genome populations. We use PacBio’s protocol for preparing multiplexed AAV SMRTbell libraries using the SMRTbell prep kit 3.0, which accommodates both self-complementing (scAAV) and single-stranded (ssAAV) constructs within a sample. Once in double-stranded form, barcoded adaptors are added onto all fragments for multiplexed sequencing.

Because AAV nucleic acids may be in multiple forms in a sample and dsDNA is required for successful sequencing, it is critical that the sample form is disclosed. This allows us to address any non-complementary and self-complementary regions with interior inserted repeats before final library preparation.

Sample Requirements:

  • Minimum of 500 ng total material
  • Maximum volume of 50 µL
  • Must declare if sample is ssAAV, scAAV, or both
  • No contact with Axygen consumables, which interfere with SMRTbell prep
  • Must be submitted on dry ice

What You Will Receive:

  • One fastq file for each sample
  • One bam file with run metric data
  • Sequencing stats summary
  • Materials and methods summary
  • Data shared via Globus within 2 weeks

Packages & Pricing

Sequencing Package Price*
Revio 25M Flowcell
Run across a Full Flowcell. Library preparation separate.		 $1,900.00
PacBio AAV Library Preparation
Includes QC and barcoding. One needed per sample. Sequencing separate.		 $300.00
*Orders >48 Samples receive 5% discount

SeqCenter offers convenient AAV extractions using ThermoFisher Scientific’s PureLink Viral RNA/DNA Mini kit. For SeqCenter to perform this service, a minimum of 7×1011 viral genomes must be submitted to meet the 500 ng requirement. Shipping must include dry ice to preserve the sample. For more information and pricing for our AAV extraction service, please contact us.

We offer AAV analysis using the open-source tool Magdoll, which is in active development by PacBio affiliated creators. A note of caution, this tool is not directly supported by PacBio itself and has not yet been peer reviewed.

In order to perform this type of analysis, the AAV backbone sequence (as a fasta file), the coordinate position from ITR to ITR, and host genome NCBI accession number must be provided. Optionally, providing the helper and Rep-Cap plasmid sequences (as fasta files) and coordinate location of the trans plasmid from ‘Rep’ to ‘Cap’ will add more information to the analysis output. The final report is delivered in pdf format.

For additional information and pricing, please contact us.

Additional Resources:

PacBio WGS

PacBio HiFi reads are ideal for WGS of complex, higher-order organisms and improve the likelihood of fully closed genomes. Library preparations are tailored to maximize read lengths for individual sample types, which helps you get the most out of your sequencing.

Explore

PacBio IsoSeq

Novel isoform discoveries are within reach with high-quality, full-length mRNA sequencing. PacBio’s unique capabilities are prime for this growing field of study, allowing for detection of novel splicing arrangements possible with no assembly or inference needed. The HiFi reads also guarantee SNP detection for each form.

Explore

Contact:
91 43rd Street, Ste. 250
Pittsburgh, PA 15201
(878) 227-4915

Services:

About:

Resources:

Full Flowcell:

We offer full flowcell sequencing services for libraries that have been prepared outside of our lab. For each library, we will need to know the loading concentration, phiX spike-in, and run structure. Data is delivered as a complete run folder and can be demultiplexed upon request if a sample sheet is provided.

SARS-CoV-2 Sequencing:

Our SARS-CoV-2 Sequencing services include an assembly on the SARS-CoV-2 reference genome as a scaffold. These packages provide roughly 200Mbp of paired end reads (2×151 bp) as fastq files and the assembly in fasta format.

We require a minimum sample volume of 15 µL of extracted material (or 250µL for VTM samples) and recommend that only samples with Ct values below 35 are sent (because submissions are not measured for viral load before processing). We offer services for both purified RNA and samples in VTM media that require viral RNA extraction. Please see our SARS-CoV-2 Sequencing page for more detailed information.

Microbiome Sequencing:

Please see our Microbiome Sequencing page for package details, including distributables and sample requirements.

Nanopore Sequencing:

Our Oxford Nanopore sequencing packages provide reads equal to the length of input DNA, delivered as a fastq file.

For each sample, we require a minimum volume of 60 µL, and at least 40 ng/µL dsDNA quantified by Qubit or other dye-based method (100 ng/µL by Nanodrop). Variant calling add-on analysis requires an annotated reference file. DNA extraction services are available for only specific categories of microbes.

Please see our DNA Sequencing: Long Read Sequencing page for more detailed information about the package, variant calling analysis, and extraction requirements.

PacBio:

Our PacBio services deliver HiFi reads with an average read length of 8-12kb for standard offerings and up to 25kb for full flowcell runs. All package names are listed by the minimum number of >Q20 reads that will be delivered. Both assembly and annotation are included with all packages.

For each sample, a minimum volume of 60 µL and at least 35 ng/µL dsDNA (quantified by Qubit or other dye-based methods) are required. SeqCenter strongly recommends utilizing our HMW DNA Extraction service for best results; however, we will also accept samples that are shipped on dry ice to avoid DNA integrity issues caused by the shipping process.

Please see our PacBio Sequencing page for more detailed information about our services.

RNA Sequencing:

We offer both rRNA depletion RNA squencing and polyA-tail enrichment mRNA sequencing. Both provide stranded, paired end reads (2x 151bp) as fastq files.

For each sample, we require a minimum volume of 20µL and at least 50ng/µL RNA. We also recommend, but do not require, that samples be DNAse treated and have a RIN score greater than 6. We also offer Basic and Intermediate RNAseq analyses, which require an annotated reference sequence.

Please see our RNA Sequencing page for more detailed information about both our RNA sequencing and analysis packages.

Illumina Sequencing:

The Illumina sequencing packages produce paired end reads (2×151 bp) delivered as fastq files.

For each sample, we require a minimum volume of 30 µL and at least 10 ng/µL dsDNA quantified by Qubit or other dye-based method (20 ng/µL by Nanodrop). Variant calling add-on analysis requires an annotated reference file. DNA extraction services are available for only specific categories of microbes.

Please see our DNA Sequencing: Whole Genome Sequencing page for more detailed information about the package, variant calling analysis, and extraction requirements.

For additional information about variant calling and short read assemblies, please see our Bioinformatics page.

Go to Top