Next GEM Flex (Fixed RNA Profiling) and GEM-X Flex Gene Expression
The Chromium™ Fixed RNA Profiling Solution produces Illumina® sequencer-ready libraries.
Please note that Dual Index Kit TS, Set A (PN-1000251) is required for use with the Fixed RNA Profiling Solution.
Compatible Sequencers
- Illumina® NovaSeq X Series
- Illumina® NovaSeq 6000
- Illumina® NextSeq 500/550
- Illumina® NextSeq 1000/2000
- Illumina® MiSeq
- Illumina® iSeq
Recommended Sequencing: Minimum 10,000 read pairs/cell*
Dual-Indexed Sequencing Run: Fixed RNA Profiling libraries are dual-indexed. We do not recommend sequencing these libraries with a single-index configuration.
PhiX Spike-In Recommendations: 1% for Singleplexed libraries, 5% for Multiplexed libraries, 10% for Multiplexed libraries on NovaSeq
| Read | Read 1 | i7 Index | i5 Index | Read 2 |
|---|---|---|---|---|
| Purpose | Cell barcode & UMI | Sample Index | Sample Index | Insert |
| Length** | 28 | 10 | 10 | 90 |
*Adjust sequencing depth for the required performance or application. The Sequencing Saturation metric and curve in the Cell Ranger run summary can be used to optimize sequencing depth.
**Shorter transcript reads may lead to reduced transcriptome alignment rates. Cell barcode, UMI and Sample index reads must not be shorter than indicated. Any read can be longer than recommended. Additional bases in Sample index reads must be trimmed using cellranger mkfastq or Illumina's bcl2fastq prior to further analysis. Additional bases in Cell barcode or UMI reads will automatically be ignored by Cell Ranger.
Next GEM Flex (Fixed RNA Profiling) Gene Expression with Feature Barcode technology for Protein using Direct Capture (TotalSeq™️-B) or Barcode Oligo Capture (TotalSeq™️-C)
Supported Sequencers
- Illumina® NovaSeq X Series
- Illumina® NovaSeq 6000
- Illumina® NextSeq 500/550
- Illumina® NextSeq 1000/2000
- Illumina® MiSeq
- Illumina® iSeq
Recommended Sequencing: Minimum 5,000 read pairs/cell*
Dual Indexed Sequencing Run: Fixed RNA Profiling Feature Barcode libraries are dual-indexed. We do not recommend sequencing 10x Fixed RNA Profiling Feature Barcode libraries with a single-index configuration.
We recommend pooling Fixed RNA Profiling Feature Barcode libraries with Fixed RNA Profiling Gene Expression libraries to maintain nucleotide diversity during sequencing.
| Read | Read 1 | i7 Index | i5 Index | Read 2 |
|---|---|---|---|---|
| Purpose | Cell barcode & UMI | Sample Index | Sample Index | Insert |
| Length** | 28 | 10 | 10 | 90 |
*Adjust sequencing depth for the required performance or application. The Sequencing Saturation metric and curve in the Cell Ranger run summary can be used to optimize sequencing depth for specific sample types.
**If sequencing Fixed RNA Profiling Protein libraries independently, they may be sequenced in the following configurations. When derived from TotalSeq™️-B antibodies (Singleplex only): 28 x 10 x 10 x 25 bp When derived from TotalSeq™️-C antibodies (Singleplex or Multiplex): 28 x 10 x 10 x 76 bp