Services

The Center for Medical Genomics offers DNA/RNA quantification, DNA quality control and fragment-size analysis, RNA quality (measure of fragmentation/degradation), and miRNA quality. DNA/RNA Analysis services include quality/quantity assessment as well as shearing and sample extraction. Instruments include NanoDrop, Agilent 4200 Tapestation, Qubit Fluorometer, and Covaris S2 Focused-ultrasonicator.

Single cell analysis includes Single Cell RNA-seq, Single Nucleus RNA-seq, Single Cell ATAC-seq, Single Cell Multiome ATAC + Gene Expression. Single Cell Immune Profiling as well as Flex Gene Expression. The center is equipped with three 10x Genomics Chromium Systems.  FAQs about single cell studies give additional details about these services.

Spatial transcriptomics is a relatively new, groundbreaking molecular profiling method that allows researchers to measure all the gene activity in a tissue sample and map where the activity is occurring. The Center for Medical Genomics offers Visium Spatial Gene Expression for FFPE and fresh frozen tissues as well as Xenium for FFPE or fresh frozen tissues. 

The Visium platform delivers unbiased, whole transcriptome spatial gene expression analysis at single cell scale with unmatched spatial data quality and offers a flexible assay portfolio to study a broad range of tissues.

Standard Visium CytAssist

Visium HD use the CytAssist workflow. HD slides contain two 6.5 x 6.5 mm Capture Areas with a continuous lawn of oligonucleotides arrayed in millions of 2 x 2 µm barcoded squares without gaps, achieving single cell–scale spatial resolution. The data is output at 2 µm, as well as multiple bin sizes. The 8 x 8 µm bin is the recommended starting point for visualization and analysis.

Sample Requirements: It is compatible with both fresh frozen and FFPE tissues. Tissue sections with RIN ≥ 4 are optimal for the fresh frozen tissue, while RNA DV200 >30%  are required for the FFPE tissues. Hydrogel coated slides are required for tissue sectioning (10uM for FF tissue, 5uM for FFPE) (provided by CMG). 

Visium HD

Visium HD use the CytAssist workflow. HD slides contain two 6.5 x 6.5 mm Capture Areas with a continuous lawn of oligonucleotides arrayed in millions of 2 x 2 µm barcoded squares without gaps, achieving single cell–scale spatial resolution. The data is output at 2 µm, as well as multiple bin sizes. The 8 x 8 µm bin is the recommended starting point for visualization and analysis.

Sample Requirements: It is compatible with both fresh frozen and FFPE tissues. Tissue sections with RIN ≥ 4 are optimal for the fresh frozen tissue, while RNA DV200 >30% are required for the FFPE tissues. Hydrogel coated slides are required for tissue sectioning (10uM for FF tissue, 5uM for FFPE) (provided by CMG). 

The Xenium platform delivers high-plex in situ at subcellular resolution with nanometer precision and offers a complete solution, including comprehensive panel offerings, to achieve fast and robust single cell spatial insights.  

Fresh, frozen or FFPE tissue is sectioned onto a Xenium slide (each slide has an imageable area of 12mm x 24mm). Specimens need to fit within the available sample positioning area measuring 235 mm2 (10.45 mm x 22.45 mm).  Sections are treated to access the RNA for labeling with circularizable DNA probes. Probe ligation generates a circular DNA probe which is enzymatically amplified. Slides are placed in the Xenium Analyzer where the sample undergoes successive rounds of fluorescent probe hybridization, imaging, and removal; creating bright, easy to image signal with a high signal-to-noise ratio.  

Sample Requirements: DAPI/HE staining is required to be done by user prior to reagent order, making sure the nuclei are intact and morphology is desired. RNA quality check for DV200 is optional. 

Pre-designed panels available for:

• Human Brain
• Human Breas
• Human Colo
• Human Immuno-Oncology 
• Human Lung 
• Human Multi-Tissue and Cancer 
• Human Skin 
• 5K Human Pan Tissue & Pathways Panel 
• Mouse Brain 
• Mouse Tissue Atlas 
• 5K Mouse Pan Tissue & Pathways Panel 

Add-on custom panels – up to 100 custom targets can be added to pre-designed panels for human and mouse. 

Fully custom panels can be designed for up to 480 genes. These are recommended when gene expression signatures differ from content in the pre-designed panels.

The Center for Medical Genomics offers whole genome sequencing, whole exome sequencing, gene panel target sequencing, DNA methylation, TELL-seq, ChIP-seq and amplicon sequencing.

RNA sequencing services include whole transcriptome sequencing, mRNA sequencing, miRNA sequencing, and targeted RNA sequencing. FAQs about RNA-sequencing give additional details about this service.

The Center for Medical Genomics offers long-read DNA and RNA sequencing on the Oxford Nanopore Technology PromethION platform. The length of an ONT read is dependent on the quality of the sample and the preparation method.  

DNA: WGS, Adaptive Sampling and Metagenomics 

RNA: Direct RNA, cDNA-PCR, direct cDNA

Sample Requirements: 

For Native DNA sequencing, we would need DNA of high quality and high quantity. Depending on the sequencing depth needed and input DNA quality, we would like to have at least 1.5 ug DNA and the ideal concentration is >=110ng/ul. If long reads are required, high molecular weight DNA should be provided, and more DNA will be needed. For DNA purity, the DNA should meet the criteria below: 

• A260/280 = 1.8 
• A260/230 = 2.0-2.2 

For direct RNA and direct cDNA sequencing, please provide at least 1.5 μg total RNA with an ideal concentration >= 120gn/ul. RNA should be o f high quality with RNA > 7. For PCR-cDNA sequencing, at least 1 μg total RNA should be provided. 

Metagenomics services include 16S sequencing and shotgun sequencing.