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Sequencing Requirements for Fixed RNA Profiling

Fixed RNA Profiling 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.

Supported Sequencers

  • Illumina® NovaSeq
  • Illumina® NextSeq 500/550
  • Illumina® NextSeq 1000/2000
  • Illumina® MiSeq

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: 5% for Multiplexed libraries; 1% for Singleplexed libraries

ReadRead 1i7 Indexi5 IndexRead 2
PurposeCell barcode & UMISample IndexSample IndexInsert
Length**28101090

*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.

Fixed RNA Profiling Gene Expression with Feature Barcode technology

Supported Sequencers

  • Illumina® NovaSeq
  • Illumina® NextSeq 500/550
  • Illumina® NextSeq 1000/2000
  • Illumina® MiSeq

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 Single Cell 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.

ReadRead 1i7 Indexi5 IndexRead 2
PurposeCell barcode & UMISample IndexSample IndexInsert
Length**28101090

*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 Cell Surface Protein libraries independently, they may also be sequenced in a 28 x 10 x 10 x 25 bp configuration.

Document Type
Specifications

Last Modified
May 25, 2022