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
Step 1 - Scheduling | Email mary-boes@uiowa.edu and andrea-sheehan@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. |
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
Submitting for QC:
For 10X cDNA:
- Prepare a 1:10 dilution. Provide both the undiluted sample and the 1:10 diluted sample.
- Bring 3 uL or more of each sample in 0.5 - 1.5 uL tubes.
- Label the tubes with your name and sample number. Indicate if it's diluted.
- Submit Bioanalyzer form and bring your samples to the Genomics Division.
For 10X Final Libraries:
- Measure concentration of libraries using Qubit HS.
- Dilute the samples to a concentration of 3 ng/uL based on the results.
- (We suggest preparing at least 25ul of the diluted sample so it's also enough for pooling and/or sequencing.)
- Bring 3 uL or more of each sample in 0.5 - 1.5 uL tubes.
- Label the tubes with your name and sample number.
- Submit Bioanalyzer form and bring your samples to the Genomics Division.
Fee Schedule
effective March 1, 2025
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 | $2,694 | $2,974 |
Each Sample 2-8 10X Genomics ATAC-Seq library | $2,182 | $2,326 |
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 Element AVITI and Illumina NovaSeq sequencing platforms.
- 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 10X Genomics-supported cell size limit is 30µm.
- 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.