Single Cell Genomics
10x Genomics Chromium Controller – High-throughput automated barcoding and library construction for powerful new RNA and DNA sequencing applications. The Chromium Controller is powered by 10x GemCode Technology and enables the encapsulation in a single run of up to 80,000+ individual cells or from as little as 1 ng of HMW gDNA into 100,000s to 1,000,000s of uniquely barcoded picoliter droplets for downstream genomic analysis with Chromium Software Suite. Chromium technical applications have revolutionized single-cell RNA-seq.
Chromium solutions include:
- Single Cell Digital Gene Expression
- Single Cell Immune Repertoire Profiling
- Digital Gene Expression and Immune Repertoire Analysis from a single cell
- Single Cell ATAC-Seq
A list of publications using 10x technology is available here. Additional educational resources including seminars, software demos, and recorded workshops can be viewed here. Datasets are also accessible from here at your convenience.
10x Genomics develop a suite of tools to analyze the DNA and RNA data produced by the Chromium controller.
- Bclprocessor: Generates special type of fastq files.
- Long Ranger: Generates high-quality haplotype phasing and structural variant calls.
- Supernova: De novo Genome assembly
- Loupe: Desktop genome browser for data visualization
- Loupe Cell Browser: Visualize and analyze 10x Chromium™ Single Cell 5′ and 3′ gene expression data
- Loupe™ V(D)J Browser: Analyze, search, and visualize V(D)J sequences and clonotypes from single cell 5′ data produced by the 10x Chromium Platform.
First time single-cell genomics users, please download the following guideline files:
Supporting documents and video links for cell preparation and project planning
Contact for Genomics and Bioinformatics Consultation
Please use this link to send an email to Dr. Magdy Alabady for consultation on new or existing Genomics and Bioinformatics projects. Also, you can contact Dr. Alabady for assistance with grant proposals and for obtaining a letter of support from GGBC.
For technical questions about existing or new Single Cell Genomics projects, please contact the following Genomics Professionals;
- Kateryna Stoianova (kstoianova@uga.edu)
- Yaravi Zuleira Suarez (yzs96757@uga.edu)
- GGBC: ggbc@uga.edu
Sample Preparation for Chromium Single Cell and nuclei RNAseq
- We can process up to 8 samples on a 10X chip at a time. The library prep cost is reflective of that and cost per sample is lowest for 8 samples. We follow 10X’s sequencing recommendations, which you can view at the link here. Read lengths can be changed as desired, but please note that shorter transcript reads can reduce alignment rates. Generally a minimum of 20,000 read pairs per cell is needed. The type and number of sequencing run(s) depends on the number of samples and coverage you need. We can make libraries with between 500 and 10,000 cells per sample, though the recommended starting point is 1,600 cells the first time you do the experiment. It is recommended to try the protocol with just one sample first before moving forward with a larger number.
- 10X has a list of demonstrated cell prep protocols at the link here. Customers should work with the tissue in their lab and provide us with a prepared cell suspension. Cell preparation methods can vary between different tissue types. Please refer to 10X’s recommendations and check the literature to find methods appropriate for your sample type. Cells are preferable in most cases, but nuclei can be used as well. Feel free to reach out to 10X or GGBC for further recommendations.
- When you submit your order and have the cell suspension ready for library prep, we need an accurate measure of cell count and viability. These QC data points are critical to the protocol working correctly. The ideal concentration is between 700-1,200 cells/uL and the viability should be >90%. An inaccurate concentration could clog the chip or result in low yield, and the presence of dead cells will reduce the recovery rate and result in a high level of noise in the data. It is also important to minimize the time from cell prep to loading the 10X chip. Customers should schedule a time with designated laboratory personnel for GEM generation. At this time, customers should bring their cell suspension and cell count/ viability. At the GGBC facility, the countess3 will be used to re-count the cells and measure viability. The measurements will be compared to the customer’s measurements and a concentration and viability will be determined for GEM processing.
- Please contact GGBC at least 2 weeks in advance before submitting a single cell order.
Table 1. 10x Genomics single cell/nuclei RNA seq library preparation fees
Number of Sample(s) UGA Fee Non-UGA Fee Commercial Fee
1 $2,758.00 $3,255.00 $3,448.00
2 $4,662.00 $5,502.00 $5,828.00
3 $6,565.00 $7,747.00 $8,207.00
4 $8,469.00 $9,994.00 $10,587.00
5 $10,622.00 $12,534.00 $13,278.00
6 $12,526.00 $14,781.00 $15,658.00
7 $14,429.00 $17,027.00 $18,037.00
8 $16,333.00 $19,273.00 $20,417.00
Table 2. Suggested Illumina sequencing run type and associated fees for single cell/nuclei RNAseq libraries
Service Description(s) UGA Fee Non-UGA Fee Commercial Fee
Library Pooling up to 2-24 samples* $60 $71 $75
Pre-Sequencing QC (Qubit, FA, Kapa) $120.00 $142.00 $150.00
NextSeq500 (150 Cycles) Mid Output flow cell $1,763.00 $2,081.00 $2,204.00
NextSeq500 (150 Cycles) High Output flow cell $3,899.00 $4,601.00 $4,874.00
NextSeq500 (75 Cycles) High Output flow cell $2,253.00 $2,659.00 $2,817.00
NextSeq2000 (100 Cycles) flow cell (P2) $2,013.00 $2,376.00 $2,517.00
NextSeq2000 (200 Cycles) flow cell (P2) $3,398.00 $4,010.00 $4,248.00
NextSeq2000 (100 Cycles) flow cell (P3) $4,040.00 $4,768.00 $5,050.00
NextSeq2000 (200 Cycles) flow cell (P3) $5,426.00 $6,403.00 $6,783.00
Table 1. 10x Genomics single cell/nuclei RNA seq library preparation fees
| Number of Sample(s) | UGA Fee | Non-UGA Fee | Commercial Fee |
|---|---|---|---|
| 1 | $2,758.00 | $3,255.00 | $3,448.00 |
| 2 | $4,662.00 | $5,502.00 | $5,828.00 |
| 3 | $6,565.00 | $7,747.00 | $8,207.00 |
| 4 | $8,469.00 | $9,994.00 | $10,587.00 |
| 5 | $10,622.00 | $12,534.00 | $13,278.00 |
| 6 | $12,526.00 | $14,781.00 | $15,658.00 |
| 7 | $14,429.00 | $17,027.00 | $18,037.00 |
| 8 | $16,333.00 | $19,273.00 | $20,417.00 |
Table 2. Suggested Illumina sequencing run type and associated fees for single cell/nuclei RNAseq libraries
| Service Description(s) | UGA Fee | Non-UGA Fee | Commercial Fee |
|---|---|---|---|
| Library Pooling up to 2-24 samples* | $60 | $71 | $75 |
| Pre-Sequencing QC (Qubit, FA, Kapa) | $120.00 | $142.00 | $150.00 |
| NextSeq500 (150 Cycles) Mid Output flow cell | $1,763.00 | $2,081.00 | $2,204.00 |
| NextSeq500 (150 Cycles) High Output flow cell | $3,899.00 | $4,601.00 | $4,874.00 |
| NextSeq500 (75 Cycles) High Output flow cell | $2,253.00 | $2,659.00 | $2,817.00 |
| NextSeq2000 (100 Cycles) flow cell (P2) | $2,013.00 | $2,376.00 | $2,517.00 |
| NextSeq2000 (200 Cycles) flow cell (P2) | $3,398.00 | $4,010.00 | $4,248.00 |
| NextSeq2000 (100 Cycles) flow cell (P3) | $4,040.00 | $4,768.00 | $5,050.00 |
| NextSeq2000 (200 Cycles) flow cell (P3) | $5,426.00 | $6,403.00 | $6,783.00 |
Table 3. 10x Genomics scATAC-seq library preparation fees
Number of Sample(s) UGA Fee Non-UGA Fee Commercial Fee
1 $2,759.00 $3,256.00 $3,449.00
2 $4,637.00 $5,472.00 $5,797.00
3 $6,515.00 $7,688.00 $8,144.00
4 $8,393.00 $9,904.00 $10,492.00
5 $10,537.00 $12,434.00 $13,172.00
6 $12,415.00 $14,650.00 $15,519.00
7 $14,293.00 $16,866.00 $17,867.00
8 $16,171.00 $19,082.00 $20,214.00
Table 4. Suggested Illumina sequencing run type and associated fees for scATAC-seq libraries
Service Description(s) UGA Fee Non-UGA Fee Commercial Fee
Library Pooling up to 2-24 samples* $60 $71 $75
Pre-Sequencing QC (Qubit, FA, Kapa) $120.00 $142.00 $150.00
NextSeq500 (150 Cycles) High Output flow cell $3,899.00 $4,601.00 $4,874.00
NextSeq500 (75 Cycles) High Output flow cell $2,253.00 $2,659.00 $2,817.00
NextSeq2000 (100 Cycles) flow cell (P2) $2,013.00 $2,376.00 $2,517.00
NextSeq2000 (200 Cycles) flow cell (P2) $3,398.00 $4,010.00 $4,248.00
NextSeq2000 (100 Cycles) flow cell (P3) $4,040.00 $4,768.00 $5,050.00
NextSeq2000 (200 Cycles) flow cell (P3) $5,426.00 $6,403.00 $6,783.00
Table 3. 10x Genomics scATAC-seq library preparation fees
| Number of Sample(s) | UGA Fee | Non-UGA Fee | Commercial Fee |
|---|---|---|---|
| 1 | $2,759.00 | $3,256.00 | $3,449.00 |
| 2 | $4,637.00 | $5,472.00 | $5,797.00 |
| 3 | $6,515.00 | $7,688.00 | $8,144.00 |
| 4 | $8,393.00 | $9,904.00 | $10,492.00 |
| 5 | $10,537.00 | $12,434.00 | $13,172.00 |
| 6 | $12,415.00 | $14,650.00 | $15,519.00 |
| 7 | $14,293.00 | $16,866.00 | $17,867.00 |
| 8 | $16,171.00 | $19,082.00 | $20,214.00 |
Table 4. Suggested Illumina sequencing run type and associated fees for scATAC-seq libraries
| Service Description(s) | UGA Fee | Non-UGA Fee | Commercial Fee |
|---|---|---|---|
| Library Pooling up to 2-24 samples* | $60 | $71 | $75 |
| Pre-Sequencing QC (Qubit, FA, Kapa) | $120.00 | $142.00 | $150.00 |
| NextSeq500 (150 Cycles) High Output flow cell | $3,899.00 | $4,601.00 | $4,874.00 |
| NextSeq500 (75 Cycles) High Output flow cell | $2,253.00 | $2,659.00 | $2,817.00 |
| NextSeq2000 (100 Cycles) flow cell (P2) | $2,013.00 | $2,376.00 | $2,517.00 |
| NextSeq2000 (200 Cycles) flow cell (P2) | $3,398.00 | $4,010.00 | $4,248.00 |
| NextSeq2000 (100 Cycles) flow cell (P3) | $4,040.00 | $4,768.00 | $5,050.00 |
| NextSeq2000 (200 Cycles) flow cell (P3) | $5,426.00 | $6,403.00 | $6,783.00 |
Table 5. 10x Genomics Single Cell Multiome ATAC + Gene Expression libraries preparation fees
Number of Sample(s) UGA Fee Non-UGA Fee Commercial Fee
1 $4,345.00 $5.128.00 $5,432.00
2 $ 7,728.00 $ 9,120.00 $ 9,660.00
3 $11,111.00 $ 13,111.00 $ 13,889.00
4 $ 14,493.00 $ 17,102.00 $ 18,117.00
5 $ 18,151.00 $ 21,419.00 $ 22,689.00
6 $ 21,534.00 $ 25,411.00 $ 26,918.00
7 $ 24,917.00 $ 29,403.00 $ 31,147.00
8 $ 28,299.00 $ 33,393.00 $ 35,374.00
Table 6. Suggested Illumina sequencing run type and associated fees for Single Cell Multiome ATAC + Gene Expression libraries
Service Description(s) UGA Fee Non-UGA Fee Commercial Fee
Library Pooling up to 2-24 samples* $60 $71 $75
Pre-Sequencing QC (Qubit, FA, Kapa)(per run) $120.00 $142.00 $150.00
NextSeq2000 (100 Cycles) flow cell(P2) $2,013.00 $2,376.00 $2,517.00
NextSeq2000 (200 Cycles) flow cell(P2) $3,398.00 $4,010.00 $4,248.00
NextSeq2000 (100 Cycles) flow cell(P3) $4,040.00 $4,768.00 $5,050.00
NextSeq2000 (200 Cycles) flow cell(P3) $5,426.00 $6,403.00 $6,783.00
Each Multiome sample produces two libraries: ATAC and 3’RNAseq. Each library requires a separate NextSeq2000 sequencing run.
Table 5. 10x Genomics Single Cell Multiome ATAC + Gene Expression libraries preparation fees
| Number of Sample(s) | UGA Fee | Non-UGA Fee | Commercial Fee | |
|---|---|---|---|---|
| 1 | $4,345.00 | $5.128.00 | $5,432.00 | |
| 2 | $ 7,728.00 | $ 9,120.00 | $ 9,660.00 | |
| 3 | $11,111.00 | $ 13,111.00 | $ 13,889.00 | |
| 4 | $ 14,493.00 | $ 17,102.00 | $ 18,117.00 | |
| 5 | $ 18,151.00 | $ 21,419.00 | $ 22,689.00 | |
| 6 | $ 21,534.00 | $ 25,411.00 | $ 26,918.00 | |
| 7 | $ 24,917.00 | $ 29,403.00 | $ 31,147.00 | |
| 8 | $ 28,299.00 | $ 33,393.00 | $ 35,374.00 |
Table 6. Suggested Illumina sequencing run type and associated fees for Single Cell Multiome ATAC + Gene Expression libraries
| Service Description(s) | UGA Fee | Non-UGA Fee | Commercial Fee |
|---|---|---|---|
| Library Pooling up to 2-24 samples* | $60 | $71 | $75 |
| Pre-Sequencing QC (Qubit, FA, Kapa)(per run) | $120.00 | $142.00 | $150.00 |
| NextSeq2000 (100 Cycles) flow cell(P2) | $2,013.00 | $2,376.00 | $2,517.00 |
| NextSeq2000 (200 Cycles) flow cell(P2) | $3,398.00 | $4,010.00 | $4,248.00 |
| NextSeq2000 (100 Cycles) flow cell(P3) | $4,040.00 | $4,768.00 | $5,050.00 |
| NextSeq2000 (200 Cycles) flow cell(P3) | $5,426.00 | $6,403.00 | $6,783.00 |
Each Multiome sample produces two libraries: ATAC and 3’RNAseq. Each library requires a separate NextSeq2000 sequencing run.
Table 7. 10x Genomics Immune Profiling 5’ GEX + V(D)J libraries preparation fees
Number of Sample(s) UGA Fee Non-UGA Fee Commercial Fee
1 $ 3,084.00 $ 3,640.00 $ 3,855.00
2 $ 5,346.00 $ 6,309.00 $ 6,683.00
3 $ 7,608.00 $ 8,978.00 $ 9,510.00
4 $ 9,871.00 $ 11,648.00 $ 12,339.00
5 $ 12,408.00 $ 14,642.00 $ 15,510.00
6 $ 14,670.00 $ 17,311.00 $ 18,338.00
7 $ 16,933.00 $ 19,981.00 $ 21,167.00
8 $ 19,195.00 $ 22,651.00 $ 23,994.00
Table 8. Suggested Illumina sequencing run type and associated fees for Immune Profiling 5’ GEX and V(D)J
Service Description(s) UGA Fee Non-UGA Fee Commercial Fee
Library Pooling up to 2-24 samples* $60 $71 $75
Pre-Sequencing QC (Qubit, FA, Kapa)(per run) $120.00 $142.00 $150.00
NextSeq2000 (100 Cycles) flow cell(P2) $2,013.00 $2,376.00 $2,517.00
NextSeq2000 (200 Cycles) flow cell (P2) $3,398.00 $4,010.00 $4,248.00
NextSeq2000 (100 Cycles) flow cell(P3) $4,040.00 $4,768.00 $5,050.00
NextSeq2000 (200 Cycles) flow cell(P3) $5,426.00 $6,403.00 $6,783.00
Each Immune Profiling sample produces two libraries: 5’ GEX and V(D)J. Each library requires a separate Nextseq2000 sequencing run.
Table 7. 10x Genomics Immune Profiling 5’ GEX + V(D)J libraries preparation fees
| Number of Sample(s) | UGA Fee | Non-UGA Fee | Commercial Fee | |
|---|---|---|---|---|
| 1 | $ 3,084.00 | $ 3,640.00 | $ 3,855.00 | |
| 2 | $ 5,346.00 | $ 6,309.00 | $ 6,683.00 | |
| 3 | $ 7,608.00 | $ 8,978.00 | $ 9,510.00 | |
| 4 | $ 9,871.00 | $ 11,648.00 | $ 12,339.00 | |
| 5 | $ 12,408.00 | $ 14,642.00 | $ 15,510.00 | |
| 6 | $ 14,670.00 | $ 17,311.00 | $ 18,338.00 | |
| 7 | $ 16,933.00 | $ 19,981.00 | $ 21,167.00 | |
| 8 | $ 19,195.00 | $ 22,651.00 | $ 23,994.00 |
Table 8. Suggested Illumina sequencing run type and associated fees for Immune Profiling 5’ GEX and V(D)J
| Service Description(s) | UGA Fee | Non-UGA Fee | Commercial Fee |
|---|---|---|---|
| Library Pooling up to 2-24 samples* | $60 | $71 | $75 |
| Pre-Sequencing QC (Qubit, FA, Kapa)(per run) | $120.00 | $142.00 | $150.00 |
| NextSeq2000 (100 Cycles) flow cell(P2) | $2,013.00 | $2,376.00 | $2,517.00 |
| NextSeq2000 (200 Cycles) flow cell (P2) | $3,398.00 | $4,010.00 | $4,248.00 |
| NextSeq2000 (100 Cycles) flow cell(P3) | $4,040.00 | $4,768.00 | $5,050.00 |
| NextSeq2000 (200 Cycles) flow cell(P3) | $5,426.00 | $6,403.00 | $6,783.00 |
Each Immune Profiling sample produces two libraries: 5’ GEX and V(D)J. Each library requires a separate Nextseq2000 sequencing run.
*Only if pooling is required