Parent Page: Research Support id: 26995 Active Page: Single-Cell and Spatial Transcriptomics id: 29414

Single Cell and Spatial Transcriptomics

The Genomics division of the Core is capable of building 10x Single Cell libraries of various types as well as 10x Spatial libraries (from Fresh-Frozen samples as well as FFPE samples).  Our new CytAssist makes FFPE tissue placement on capture areas more accurate, and it also allows us to use previously placed and stained tissue sections.  Our NextSeq 2000 enables us to sequence all library types in house at an increased turnaround time.  Please schedule a time to talk with us about your project needs by contacting Jenny Gipson at 405-271-2337 ext. 32514 or emailing: or

Sample Submission Instructions

Single Cell RNA-Seq

  • cells should be live dead sorted, and a test sort should be run on your samples prior to submission date to make sure you are getting the number of cells and viability needed
  • cells should be at 70% viable or greater
  • a date for the experiment must be set beforehand so that all library building reagents are in the lab and time can be devoted to handling your samples
  • please have cells ready by 1pm.  If you need to submit cells later than 1pm, please schedule that with the genomics personnel
Spatial Transcriptomics
  • fresh-frozen tissue samples can be processed without the CytAssist
  • all samples processed on the CytAssist must be FFPE samples and can be freshly sectioned or previously sectioned and even stained
  • the CytAssist eliminates the need to score blocks in order to fit into the capture areas
  • capture area sizes are either 4 sets of 6.5mm or 2 sets of 11mm
  • FFPE samples need to be previously processed for RNA to determine RNA quality before the experiment.  FFPE quality must be >30% DV200.

On-line Submission Instructions

Request services by logging onto the Institutional Research Core Facility site via our iLab Solutions portal:

If you do not already have an account, please click on the "Register" button in the upper right corner.

If you are an internal user, log in using your OUHSC username and password.   Once you have logged in, please request the service of your choice.  If you have any questions, please email us at

Current Pricing


Single Cell Library Preparation (sequencing prices below)


  Internal Pricing  

  External Pricing Industry Pricing
10x Single Cell 3' RNA Library Prep


   $3,275.00/sample       $4,275/sample  
Fixed RNA Library Prep *inquire    
Other 10x Single Cell Library Prep *inquire    


Spatial Transcriptomics (sequencing prices below)

Service Internal Pricing           
External Pricing            Industry Pricing             
10x Visium Spatial Transcriptomics (without CytAssist), 4 x 6.5mm   $6,705.00/slide   $7,912.00/slide   $8,912.00/slide
10x Visium FFPE Spatial Transcriptomics, Mouse (without CytAssist), 4 x 6.5mm   $6,750.00/slide   $7,965.00/slide   $8,965.00/slide
10x Visium FFPE Spatial Transcriptomics, Human (without CytAssist)   *inquire    
10x Visium FFPE Spatial Transcriptomics, Mouse   *inquire    
10x Visium FFPE Spatial Transcriptomics, Human   *inquire    


Service Internal Pricing External Pricing Industry Pricing
Bulk Sequencing per Million reads   $6.00/M    $8.70/M    $18.00/M 
Single Cell, minimum 20,000 reads/cell  *inquire    
10x Visium, minimum 25,000 read pairs per tissue covered spot
*6.5mm - 4,992 spots
*11mm - 14,336 spots

Basic Bioinformatic Analysis

Service Internal Pricing External Pricing Industry Pricing
1-5 samples  $200/sample  $300/sample  *inquire
6-10 samples  $150/sample  $225/sample  *inquire
11-20 samples  $100/sample  $150/sample  *inquire
21+ samples  $50/sample  $75/sample  *inquire