Services Core/Facility: Keck Microarray Shared Resource

Single-cell genomics and proteomics analysis: 10x Genomics

Services to study cellular heterogeneity at the single-cell level.

Available to Yale researchers & external researchers

Core Website
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About the service

Single cell genomic and proteomic (multiomics) is one of the most fast-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.

10x Genomics Chromium Controller


KMSR has been offering 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 version of the chemistries and assays. it has been 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 turn-key software analysis tools that enable the discovery of previously inaccessible genetic information at 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.




Sample submission


Project consultation: We strongly recommend a consultation meeting before starting your first sngle-cell project. Consultations are free for 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 24-48 hours before submission, but we cannot guarantee availability.

To schedule a submission appointment, please contact Meg Palmatier at

Sample Submission – To submit 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.

Sequencing request


To request sequencing at Yale Center for Genome Analysis with the prepared library, please use WiKiLIMS system.


Non-Yale investigators

Please contact with the details of your project (or call 203-737-3031) and you will be forwarded to the appropriate manager.

Once your workflow fully transitions to the wiki, you will be able to track sample progress in real time by either logging in or by automatic email updates.

The site works best using the LATEST version of Firefox or Chrome.

New users

New users: kindly request an account here and bookmark the page.


Rates as of 7/1/23

ServiceYale userNon-Yale user
10x single cell RNA-Seq library prep (5P/3P/ATAC/CNV)$1760$2289
10x single-cell VDJ/Feature barcoding library prep$135$178
10x single-cell RNA-Seq library prep w/o GEM reagents$314$425
10x multiome RNA and ATAC-seq library prep$3165$4120
10x single-cell flex multiplex (4-plex minimal, per sample)$1788$2358
10x single-cell flex singleplex$2562$3776
10x single-cell flex single plex feature barcoding$247$340
10X single-cell HT (5P/3P, 8 samples minimal)$2531$3700
10x targeted gene expression library prep$842$1108
10x nuclei isolation$250$4120