10x Genomics Chromium

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 and 10x Linked-Read technology now provides long-range information from short-read sequencing data.

Chromium solutions include:

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.
Consultation and Assistance

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.

Contact for 10x Genomics Technical Assistance
For technical questions about existing or new 10x Genomics projects, please contact the following Lab Managers:

Sample Preparation

Sample preparation

For the genomics application, high quality HMW DNA is required. DNA will be tested on the Fragment Analyzer using the 50Kb protocol and, if needed, on the PippinPuls (a PFGE system).

10X Genomics recommendations for specific HMW DNA isolation protocols can be accessed from here.

  • DNA should be above 50kb with greater than 80% of the DNA at 100kb or larger. After isolation, the DNA should be handled very gently (minimal pipetting, use of wide-bore tips, avoid freeze/thaw, etc).
  • Ship HMW DNA on dry ice for stability, but once it arrives at the GSL it will be stored at 4C.
  • Though the protocol uses 1ng of HMW DNA as input, a minimum of 500ng of DNA in 20ul of water or Tris should be submitted to allow for QC and visualization of the HMW DNA on a gel.
  • If you are are submitting 24 or more samples please submit samples in a 96-well plate and include an Excel file with the sample layout in your order.
  • PLEASE USE V BOTTOM PLATES AND NOT ROUND/FLAT BOTTOM PLATES.
Chromium Data and Sequencing

Chromium libraries have a unique structure that requires special sequencing considerations. Each DNA sample is indexed with four i7 barcodes sequenced as a standard i7 index read of 8bp in length. Each i7 barcode is a combination of 8-bases unique barcodes. The unique barcode used to link reads is found at the beginning of read 1 and is 16bp in length.

Chromium Linked-reads

  • 10X Genomics recommend 30-40X for whole genome resequencing projects and 40-56X coverage for de novo assembly of genomes.
  • At GGBC, we typically sequence 10X Genomic library on a NextSeq PE150 High Output run. The yield of this run is about 110-120b and 85% of the bases are >= Q30. Because the i7 barcodes are unique, two 10X libraries can be multiplexed and sequenced on the same flowcell.

Chromium Single Cell and nuclei RNAseq

  • <Coming Soon>
Prices and Quotes

Contact for Financial Inquiries and Quote Requests

Please email Kim and Elizabeth at ggbc@uga.edu, for financial inquiries or to request a quote. Be as specific as possible, so that they can more quickly assist you.

Table 1. 10x Genomics linked-reads library preparation fees

Number of Sample(s)UGA FeeNon-UGA FeeCommercial Fee
1$685.00$809.00$1,028.00
2$1,105.00$1,304.00$1,658.00
3$1,525.00$1,800.00$2,288.00
4$1,945.00$2,296.00$2,918.00
5$2,500.00
$2,950.00$3,750.00
6$3,220.00$3,800.00$4,830.00
7$3,940.00$4,650.00$5,910.00
8$4,660.00$5,499.00$6,990.00

Table 2. Suggested Illumina sequencing run type and associated fees for linked-reads libraries

Service Descrption(s)UGA FeeNon-UGA FeeCommercial Fee
Library Pooling up to 2-24 samples by qPCR*$129.00$153.00$194.00
Pre-Sequencing QC (Qubit, FA, Kapa)$61.35$72.45$92.05
NextSeq (300 Cycles) Mid Output flow cell $2,269.00**$2,678.00$3,404.00
NextSeq (300 Cycles) High Output flow cell$5,283.00**$6,234.00$7,925.00

*Only if pooling is required
**Additional 5% discount available for UGA customers doing 10 or more NextSeq runs between 7/01/17 and 6/08/18. Click here for more details.

Table 3. 10x Genomics single cell/nuclei RNA seq library preparation fees

Number of Sample(s)UGA FeeNon-UGA FeeCommercial Fee
1$1,776.00$2,096.00$2,664.00
2$3,204.00$3,781.00$4,806.00
3$4,632.00$5,466.00$6,948.00
4$6,060.00$7,151.00$9,090.00
5$7,706.00
$9,094.00$11,559.00
6$9,434.00$11,133.00$14,151.00
7$11,162.00$13,172.00$16,743.00
8$12,890.00$15,211.00$19,335.00

Table 4. Suggested Illumina sequencing run type and associated fees for single cell/nuclei RNAseq libraries

Service Descrption(s)UGA FeeNon-UGA FeeCommercial Fee
Library Pooling up to 2-24 samples by qPCR*$129.00$153.00$194.00
Pre-Sequencing QC (Qubit, FA, Kapa)$61.35$72.45$92.05
NextSeq (150 Cycles) Mid Output flow cell $1,560.00**$1,841.00$2,340.00
NextSeq (150 Cycles) High Output flow cell***$3,448.00**$4,069.00$5,172.00
NextSeq (75 Cycles) High Output flow cell$1,993**$2,352.00$2,990.00

*Only if pooling is required
**Additional 5% discount available for UGA customers doing 10 or more NextSeq runs between 7/01/17 and 6/08/18. Click here for more details.
***Recommended run type