Single-cell genomics and proteomics analysis
Primary contact
About the service
10x Genomics
Single-cell genomics and proteomics (multiomics) is one of the fastest-moving research and development areas in recent years. KMSR has been keeping pace with the advancement and offering a variety of services to study cellular heterogeneity at the single-cell level.
KMSR has offered single-cell genomics analysis since 2016. The first system we acquired was from 10x Genomics, Chromium Controller, which can do linked-reads and single-cell DNA analysis as well as single-cell RNA-seq. Since then, we have been keeping the services updated with the latest versions of the chemistries and assays. It has gradually evolved into a major platform for multiomics analysis with both low-throughput (200-1000 cells) and high-throughput (10,000 to 20,000 cells) options.
The Chromium™ System developed by 10x Genomics is a unique reagent delivery system that can partition cells with a massive diverse barcode library to generate >100,000 barcode-containing partitions in a matter of minutes. It enables simple workflow from cell suspension through cDNA sequencing and analysis that is more efficient than leading academic droplet systems. It can encapsulate up to 48,000 cells in 10 minutes and can be used to identify rare cell types in heterogeneous populations with wide dynamic range.
The Chromium system is powered by 10x GemCode technology
The 10x GemCode technology fuels our Chromium system with an innovative reagent delivery system, set of algorithms, and turnkey software analysis tools that enable the discovery of previously inaccessible genetic information at a massive rate and scale.
GemCode creates a unique reagent delivery system that partitions cells or arbitrarily long DNA molecules (including 100 kb) and prepares sequencing libraries in parallel such that all fragments produced within a partition share a common barcode.
A simple workflow combines large partition numbers with a massively diverse barcode library to generate 100,000 barcode-containing partitions in a matter of minutes. It is a fully integrated solution for RNA and DNA analysis.
Parse Biosciences
The cell is the reaction vessel
The Evercode™ solution from Parse Biosciences converts each cell or nucleus into an individualized reaction compartment. This approach steps away from the limitations of hardware-based offerings by evolving the assay for a more elegant, simple solution to single-cell (scRNA-Seq) and single-nuclei sequencing (snRNA-Seq).
Fix now, run later
Fix cells or nuclei as they're available to lock in the biology. After a 30-minute fixation, samples are stable for 6 months. Whether working on a timecourse study, sharing samples between laboratories, or segregating sample preparation from core lab space, fixation provides the flexibility to work the way you desire.
No instrument required
Conventional droplet-based single-cell technologies struggle as cell or experiment sizes change. Parse makes it easy to scale your experiments regardless of cell size or sample type. The Evercode™ split-pool combinatorial barcoding technology, originally based on the approach published in Science and known widely as SPLiT-Seq, is accessible to any standard biology lab.
BD Rhapsody
The BD Rhapsody™ Express System enables single-cell capture and barcoding of hundreds to thousands of single cells for analysis of genomic and proteomic information, using proprietary, gentle, robust microwell-based single-cell partitioning technology. The BD Rhapsody™ Express System can be used for lower scale experiments or throughput needs versus the NEW BD Rhapsody™ HT Xpress System, our NEW platform for flexible and scalable experimental design and higher throughput cell and sample inputs. The BD Rhapsody™ Express System is also ideal for routine use with familiar cell systems that do not require visual QC or troubleshooting.
Isospark
The IsoSpark system measures the true function of each cell and identifies the rare subsets of highly functional cells driving response.
- Single-cell secretome: Actively secreted proteins (cytokines and chemokines) at single-cell resolution of live cells for functional phenotyping
- Single-cell signaling: Assessment of the phosphoproteome spanning multiple signaling pathways at single-cell resolution.
- Bulk proteomics: Automated bulk protein analysis of cell-free, protein-containing biological solutions (e.g., cell supernatant, serum, plasma, CSF, etc.)
Available to Yale researchers & external researchers
Specifications
Sample submission
Project consultation: We strongly recommend a consultation meeting before starting your first single-cell project. Consultations are free to investigators utilizing the KMSR's single-cell service. To request a meeting, please contact Guilin Wang.
Scheduling your experiment: The single-cell service is by appointment only. You must have an appointment prior to submitting samples. Submission appointments should be made a minimum of one week in advance of your anticipated submission date. This prevents scheduling conflicts and ensures the appropriate reagents are available and at the correct temperatures for immediate use (having samples sit while we bring reagents to temperature may negatively impact data). We will make effort to accommodate appointments made 24 to 48 hours before submission, but we cannot guarantee availability.
To schedule a 10x Genomics submission appointment, please contact Meg Palmatier.
To submit 10x Genomics samples, please complete a 10x Genomics Single Cell Service Request Form. For Yale local users, please bring the form to 300 George Street, room 2127 at the scheduled time with your samples. For external investigators, please contact Guilin Wang.
To schedule a Parse submission appointment, please contact Evelyn Ng.
To submit Bruker IsoSpark System samples, please contact Guilin Wang.
Sequencing request: To request sequencing at Yale Center for Genome Analysis with the prepared library, please use iLab.
Non-Yale investigators
Please contact ycga@yale.edu with the details of your project (or call 203-737-3031) and you will be forwarded to the appropriate manager.
Rates
Rates as of July 1, 2026
| Service | Yale user |
|---|---|
| 10x single-cell RNA-Seq library prep (5P/3P/ATAC) | $1,780 |
| 10x single-cell VDJ/Feature Barcoding library prep | $165 |
| 10x single-cell RNA-Seq library prep w/o reagents | $370 |
| 10x multiome RNA and ATAC-seq library prep | $3,200 |
| 10x single-cell Flex single plex (1-3 samples, per sample) | $2,780 |
| 10x single-cell Flex feature barcoding library prep | $450 |
| 10x single-cell flex 16-plex library prep (>16 samples, per sample) | $750 |
| 10x single-cell flex 8-plex library prep (8-15 samples, per sample) | $850 |
| 10x single-cell flex 4-plex library prep (4-7 samples, per sample) | $1,788 |
| 10x nuclei isolation (with RNAse inhibitor, per sample) | $340 |
| 10x nuclei isolation (without RNAse inhibitor) | $160 |
| 10x OCM gene expression library prep (per sample, 4 samples minimum) | $835 |
| 10x OCM library prep w/o reagents (per sample, 4 samples minimum) | $225 |
| Data analysis | $335 |
Non-Yale users: Price upon inquiry.
| Services | Yale user |
|---|---|
| ParseBio scRNA library prep (starting from cDNA*, per 10k cells, without reagents) | $430 |
*If the library prep is starting from fixed cells, the first library prep cost would be $860 for Yale users. Subsequent libraries would be $430 each for Yale users.
| Please contact Guilin Wang for service fees. |
Invoicing and payment
Visit our invoicing and payment page for instructions.