Frequently asked questions
- Our shipping address is:
SeqCoast Genomics LLC
25 New Hampshire Ave.
Portsmouth, NH 03801
Phone: (603) 259-4452
- We will notify you when your samples are received by the SeqCoast Lab.
- Please be sure that your well-sealed tubes and plates are clearly labeled using permanent ink and include a copy of the order confirmation with your samples.
- DNA samples can be shipped overnight at ambient temperature, but during warmer months shipping with ice packs is recommended. You may also send your samples frozen on dry ice if you prefer.
- Samples requiring nucleic acid extraction should be sent as sealed, pre-grown agar plates at room temperature or as frozen cell pellets on dry ice.
- For all shipments, please ship your samples in a rigid box and/or multiple packaging layers to protect them during transit. Follow instructions from your shipping vendor for proper packaging of dry ice.
- We recommend sensitive samples be shipped Monday-Wednesday for overnight delivery to avoid delays on weekends. We are not responsible for samples lost, delayed, or damaged in shipping. We will send confirmation of receipt.
- We will retain extracted DNA for 6 months in case you decide to perform additional sequencing.
- DNA extraction: many column-based extraction kits provide good results, as do other methods if care is taken to remove contaminants. Our library prep methods work best with buffers containing less than 1mM EDTA.
- RNA extraction: we recommend Qiagen RNeasy kits with DNase treatment, or similar.
- Metagenomic DNA samples: we recommend a physical lysis method such as bead beating to preserve community diversity.
- Long read sequencing: we strongly recommend sending raw samples for us to extract nucleic acids composed of longer fragments for better service.
We recommend Qubit or other fluorescent dye-based measures of nucleic acid quantification, or Bioanalyzer/Tapestation. Nanodrop is also acceptable, though we ask that you aim to supply well above the requested 10ng/ul minimum as this technology tends to overestimate concentrations by as much as 10-fold. When Nanodrop and Qubit values are discordant this is often an indication of contaminants such as phenol or ethanol, which can sometimes interfere with NGS workflows.
Please don’t hesitate to contact us with questions about this important decision. Here are a few guidelines:
- Variant calling, or mutation detection in comparison with a reference genome, typically requires a minimum of 30x mean coverage. Converting this to our offerings, multiply [desired coverage] x [genome size, in Mb].
- For genome resequencing projects, we strongly encourage including your wild-type strain along with your test samples.
- For de novo hybrid assembly, we recommend at least 50X short reads and 30X long reads.
You can expect to receive your sequencing data within 15 days of receipt of your samples, if not sooner. You will receive an email confirmation of receipt and a projected delivery date for your order.
Within your folder, you will find compressed FASTQ files for each sample (2 per sample for paired end reads), a README of methods, sample QC files, and any analysis services you requested in a separate directory.
We accept purchase orders and all major credit cards. Credit card orders incur a processing fee to offset a portion of the fee imposed by the card processor (Stripe). We also accept wire transfers with a $30.00 surcharge for incoming bank fees and, for international wire transfers, an additional $30.00 surcharge if your institution deducts their outgoing wire fees from the amount due.
16S is used to profile microbial communities. Full-length 16S sequencing (Nanopore) yields higher resolution of species and strains compared to V3/V4 sequencing (Illumina).
16S rRNA sequencing is used to examine bacterial species diversity and abundance of a microbial community. The 16S rRNA gene is a well-established marker for bacterial species, and it consists of both conserved regions and hypervariable regions (V1-V9). Primers bind to the conserved regions, and the hypervariable regions are amplified, sequenced, and analyzed.
Because the entire 16S sequence is over 1500bp long, only a subset of the sequence can be revealed using Illumina sequencing. We use primers 341F and 806R to amplify the V3/V4 hypervariable regions, and we perform 2x300bp paired end sequencing. This sequence length allows the paired reads to overlap, maximizing accuracy. Still, Illumina sequencing often fails to resolve species or strain-level differences. If this level of detail is important for your project, use our Nanopore full-length 16S service to sequence and analyze the entire 16S gene!