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Extraction Services

SeqCenter offers high‑quality DNA and RNA extraction services to support all Illumina, PacBio, Oxford Nanopore, and amplicon workflows. Our extraction methods are optimized for microbial, viral, metagenomic, and long‑read applications, and can be added to any sequencing project. All extractions are performed in‑house using validated kits and automated instrumentation to ensure consistent yields and excellent downstream sequencing performance.

Packages & Pricing

Service Description Price
DNA Extraction Standard genomic DNA extraction for microbial and low‑complexity samples. $15.00
RNA Extraction Total RNA extraction for RNA‑seq and metatranscriptomics. $20.00
HMW DNA Extraction High‑molecular‑weight DNA for PacBio HiFi and Oxford Nanopore long‑read sequencing. $50.00
AAV Extraction Extraction optimized for AAV vector genomes. Contact Us
TissueRuptor Add‑On Mechanical disruption for tough or fibrous samples. Contact Us
Custom Extraction For specialized workflows; quoted per project. Contact Us

Sample Requirements

(all live samples must adhere to BSLII+ safety standards)

DNA Extraction

1–2 mL culture, cell pellet, or environmental sample. For HMW DNA, avoid vortexing or harsh mechanical disruption.

RNA Extraction

Fresh or frozen biomass. RNase‑free handling recommended. For viral RNA: ≥250 µL VTM or ≥15 µL purified RNA.

Why SeqCenter

  • Fast turnaround
  • Consistent, validated workflows
  • Kits selected for sequencing compatibility
  • Support for both short‑read and long‑read platforms
  • Microbial and viral extraction expertise
  • Transparent pricing

Where Extraction Is Available

Extraction services can be added to any of the following sequencing workflows:

Illumina
PacBio
Oxford Nanopore

Extraction Methods

DNA Extraction

Our standard DNA extraction workflow uses the ZymoBIOMICS DNA MiniPrep Kit, which provides unbiased microbial lysis through mechanical bead‑bashing. This method produces high‑purity DNA suitable for whole‑genome sequencing, 16S/ITS amplicons, and shotgun metagenomics.

For high‑throughput projects, we also offer automated extraction using the EZ2 Connect platform. Magnetic‑bead purification ensures consistent yields and reduces hands‑on time, making it ideal for larger sample sets.

RNA Extraction

RNA extraction is available for RNA‑seq, metatranscriptomics, and viral sequencing workflows. We use the Quick‑RNA Miniprep Plus Kit, which includes on‑column DNase treatment and efficiently recovers both large and small RNA species. This method is compatible with a wide range of biomass types, including microbial cultures and environmental samples.

High‑Molecular‑Weight DNA Extraction

For long‑read sequencing, we use PacBio’s Nanobind PanDNA kit to isolate ultra‑long, high‑purity DNA with minimal shearing. This method is recommended for PacBio HiFi and Oxford Nanopore projects where read length and structural variant resolution depend on intact genomic fragments.

AAV Extraction

Our AAV extraction workflow is optimized for viral vector genomes and is compatible with downstream sequencing, QC, and titer confirmation. This service is recommended for gene therapy and vector development projects.

TissueRuptor Add‑On

Some samples require additional mechanical disruption. The TissueRuptor add‑on improves lysis efficiency for tough bacterial strains, biofilms, environmental samples, and fibrous tissues. This add‑on can be only combined with HMW extractions.

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.

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