10X Genomics Chromium Single-Cell System

The 10X Genomics Chromium Single-Cell System is used to provide a single-cell expression profiling technology that allows for high-throughput single cell transcriptomics of many different cell types as well as single-nuclei expression profiling. The flexible workflow encapsulates 100 to 10,000 cells or nuclei per library together with micro-beads into nano-droplets.  Each bead is loaded with adapters containing one of 750,000 different barcodes for the single cell RNA-seq library preps.  Up to eight samples can be processed per batch. The resulting data can be analyzed with the free Cell Ranger and Loupe Cell Browser software. In addition the IIHG Bioinformatics Division has developed a custom single-cell data analysis pipeline for 10X data. 

The service operates the 10X Genomics Chromium X and iX Controllers. These controllers support Single-Cell Gene Expression, Immune Profiling,  ATAC, and other assays that are supported by the Chromium X controllers. These assays include the measurement of gene expression, cell surface proteins, immune clonotype, antigen specificity, and/or chromatin accessibility.

Fee Schedule

 

There are two service workflows available:

Full-Service

Our staff will prepare the single-cell (or nuclei) RNA-seq libraries from cell/nuclei suspension samples submitted by the research labs.  Since the samples should be processed as quickly as possible, these experiments need to be planned and scheduled well in advance with our staff. 

Self-Service

The investigator performs all the necessary steps to prepare their single-cell libraries for sequencing.  This option may be beneficial if your lab is planning a large number of single-cell experiments or if it is difficult to plan well in advance when your cells would be ready.

 

Single-Cell Full-Service Workflow

Full-Service Workflow
Step 1 - Scheduling
Email garry-hauser@uiowa.edu and mary-boes@uiowa.edu.
Step 2 - Prepare Samples
Suspend cells in PBS with 0.04% non-acetylated BSA or other 10x approved buffer/media.
Cell viability should be >90% (minimum 70%).
Contact us at least 30 minutes before you bring your cells/nuclei.
Step 3 - Fill out the form
Complete the 10x Single Cell Full Service Workflow form -  Single Cell Full Service Submission Form.xlsx.
Step 4 - Drop off your samples
Bring the completed and printed sample submission form.
Arrive with your samples before 2:00pm on the day you are scheduled.

 

 

Single-Cell Self-Service Workflow

Single Cell Self-Service Workflow

 

 

Fee Schedule (effective July 1, 2024) 

 

Full service LIBRARY PREP*

Single-Cell library type

Campus

Off-campus

First Sample 10X Genomics 3' GEX v4
$2,717
$3,045
          Each Sample 2-8 10X Genomics 3' GEX v4
$1,797
$1,821
First Sample 10X Genomics 5' GEX v3  
$2,795
$3,123
          Each Sample 2-8 10X Genomics 5' GEX v3 
$1,875
$2,019
First Sample 10X Genomics 5'GEX +V(D)J 
$3,136
$3,608
          Each Sample 2-8 10X Genomics 5' Expression +V(D)J 
$2,240
$2,384
First Sample 10X Genomics V(D)J library
$2,770
$3,098
          Each Sample 2-8 10X Genomics V(D)J library
$2,162
$2,306
First Sample 10X Genomics library FAILED
$2,367
$2,551
          Each Sample 2-8 10X Genomics library FAILED
$2,047
$2,191
First Sample 10X Genomics ATAC-Seq library
$2,644
$2,924
          Each Sample 2-8 10X Genomics ATAC-Seq library
$2,132
$2,276
First Sample 10X Genomics Multiomics library
$4,463
$4,887
          Each Sample 2-8 10X Genomics Multiomics library
$3,663
$3,807

 

Self-Service LIBRARY PREP* 

Use of 10x controller and cartridge holder
$245/run
QA/QC via Bioanalyzer or TapeStation
$12/sample
*The fees in these tables reflect the cost of library prep only. Sequencing fees are a separate charge.

10X Chromium Single Cell Features:

  • Fast workflow from cell suspension to 3′ or 5’-cDNA libraries, and T or B cell V(D)J analyses.
  • Captures 100-80,000+ cells (from up to 8 samples) in < 7 minutes.
  • Recovers up to ~65% of cells (typically 50%).
  • Low doublet rate (~0.9% per 1,000 cells).
  • Compatible with Illumina NovaSeq 6000 and MiSeq sequencers.
  • The 10X Single-Cell libraries are most economically sequenced on our Illumina NovaSeq 6000.
  • At least 20,000 reads per cell (or nuclei) should be targeted for sequencing.
  • It is possible to work with cryo-preserved cells, enabling safe sample shipping and batching.
  • The cell size limit is comparatively high.  Cells can have a diameter of up to 50 µm.
  • In addition to cell suspension samples, nuclei suspensions can also be used.  For information regarding sample preparation, please refer to the 10X cell preparation guide.