Answer: As part of the 10x Genomics Compatible Partner Program, the following 10x Genomics library types have been verified as compatible with sequencing on the Ultima Genomics UG 100™ Sequencer, after conversion to add Ultima Genomics adapters:
- Universal 3’: Gene Expression libraries (GEM-X v4, Next GEM v3.1)
- Universal 5’: Gene Expression libraries (GEM-X v3, Next GEM v2)
- Flex: Gene Expression libraries (GEM-X and Next GEM, Singleplex and Multiplex)
- Visium HD: Spatial Gene Expression libraries
Resources
Additional details regarding compatibility testing can be found in the following Ultima Genomics Technical Notes:
- Fully integrated 10x Genomics single cell and spatial transcriptomics workflows with Ultima Genomics UG 100™ Sequencing Platform (published February 2025)
- Enabling single cell RNA-seq at scale on the Ultima Genomics UG 100™ Sequencer (published 2022)
Example datasets from 10x Genomics libraries sequenced on the Ultima UG 100 Sequencer can be found here:
- Visium HD Spatial Gene Expression Library, Human Breast Cancer (Fresh Frozen), Ultima Sequencing
- Visium HD Spatial Gene Expression Library, Human Tonsil (Fresh Frozen), Ultima Sequencing
Select publications:
Library Conversion
10x Genomics libraries contain Illumina P5 and P7 adapters, as well as Illumina Read 1 and Read 2 sequencing primer binding sites. When sequencing on non-Illumina short read sequencing platforms, 10x Genomics libraries must be modified to append different adapter sequences.
The Ultima Genomics Indexing PCR Library Preparation Protocol for Solaris Flex (D1001055) can be used to append Ultima Genomics-compatible adapter sequences, as described in the Ultima Genomics Technical Note. Protocols are located in the Ultima Genomics Resource Center.
Library conversion primers anneal to the Read 1 and Read 2 sequences in 10x Genomics libraries and contain Ultima Genomics adapter sequence overhangs and sample indexes. Different library conversion primers are needed for different 10x Genomics library types, depending on which Read 1 and Read 2 sequences they contain:
- Universal 3’ and 5’ Gene Expression libraries are generated using 10x Genomics Dual Index Plate TT. For the compatibility testing above, Ultima Genomics library conversion primers were used that anneal to TruSeq Read 1 and TruSeq Read 2 (conversion primers UG-tR1 and UG-tR2)
- Flex and Visium HD Gene Expression libraries are generated using 10x Genomics Dual Index Plate TS. For the compatibility testing above, Ultima Genomics library conversion primers were used that anneal to TruSeq Read 1 and TruSeq Small RNA Read 2 (conversion primers UG-tR1 and UG-srR2)
The library conversion primers mentioned above are expected to be suitable for other 10x Genomics library types that use 10x Genomics Dual Index Plate TT or TS; however, library types other than the ones listed above have not been verified by 10x Genomics for sequencing on the UG 100. Different conversion primers would be required for libraries generated using 10x Genomics Dual Index NT, TN, NN plates; these primers have not been verified by 10x Genomics. Contact Ultima Genomics for more information regarding conversion primers. Refer to this linked article for a list of which index plate is used for each 10x Genomics library type.
Conversion and sequencing of 10x Genomics libraries on the UG 100 Sequencer requires third-party reagents and third-party protocols. Contact Ultima Genomics for guidance and troubleshooting related to library conversion protocols, sequencing configurations, sequencing primers, library pooling, and sequencing performance.
Data analysis
For data analysis, the single-end reads generated during UG 100 Sequencing must be split into two FASTQ files corresponding to Read 1 and Read 2 prior to running 10x Genomics pipelines. This can be performed on the UG 100 as part of the on-instrument data processing, as described in the Ultima Genomics Technical Note. Contact Ultima Genomics for questions regarding FASTQ generation and splitting. Each 10x Genomics software pipeline has its own requirements for sequencing lengths. Please see product-specific pages for further information on FASTQ file input requirements:
For questions related to running 10x Genomics software, contact support@10xgenomics.com.
Products: Single Cell Gene Expression, Single Cell Immune Profiling, Single Cell Gene Expression Flex, Visium HD