SGT Resources

We measure DNA concentrations with Qubit and band sizes for possibly degraded DNA with the Agilent Bioanalyzer. Here is quick refresher on genomic DNA quantity and quality.
*Please note: NanoDrop Spectrophotometers can overestimate concentrations. Take this into consideration if submitting samples that have been quantified this way.

For Illumina sequencing, we recommend the following kits for genomic DNA extractions:

• Standard genomic DNA - Qiagen DNeasy
• QIAamp DNA FFPE Tissue Extraction

For long read sequencing, we recommend the following kits for high molecular weight genomic DNA extractions:

• NEB Monarch HMW DNA Extraction
• PacBio Circulomics HMW DNA Extraction
• MagAttract HMW DNA Kit

We measure RNA concentrations with Qubit and band sizes with the Agilent Bioanalyzer. Here is a quick refresher on RNA quality. We strongly recommend DNase treatment on RNA samples.
*Please note: NanoDrop Spectrophotometers can overestimate concentrations. Take this into consideration if submitting samples that have been quantified this way.

We recommend the following kits for RNA extractions:

• QIAamp Viral RNA Mini Kit
• RNeasy Plus Mini Kit
• miRNeasy Serum/Plasma Kit

Multiple samples can be indexed by a unique nucleotide sequence and pooled into an individual run to save costs. Samples may be indexed using Illumina’s TruSeq indices, Nextera indices, or custom indexing adaptors. The SGT can demultiplex the reads and provide fastq files for each individual sample if Illumina indices are used.
*Please note: If submitting customer prepared libraries, each library must contain a unique index barcode to allow for pooling and accurate demultiplexing. Indexes cannot be reused for libraries in the same pool.

The NovaSeq X Plus is a the latest robust and flexible, production-scale sequencer from Illumina that utilizes patterned flow cells and novel 2-color channel XLEAP chemistry. XLEAP chemistry reduces reagent costs and decreases data processing times while still producing the same high-quality data. The NovaSeq X also allows the flexibility to sequence by flow cell or lane.

SEQUENCING OUTPUT PER FLOW CELL

The MiSeq is a benchtop sequencer from Illumina that allows for more focused applications, such as targeted gene sequencing, metagenomics, small genome sequence, targeted gene expression, and amplicon sequencing. The ability to run long paired-end reads (2 x 250bp or 2 x 300bp) makes this instrument ideal for amplicon sequencing. The MiSeq is capable of generating ~12 million reads passing filter for v2 kits (~24 million for paired-end sequencing) and ~22 million reads passing filter for v3 kits (~44 million for paired-end sequencing).

The NextSeq 1000 is a new benchtop sequencer from Illumina that utilizes a patterned flow cell, 2-color channel chemistry, and an integrated sequencing cartridge. The patterned flow cell features a novel, high resolution optical system and higher cluster densities to allow for increased data output with greater resolution. Two flow cell types are offered to help cater to coverage needs: P1 and P2.