The Single Cell RNA analysis pipeline provides compatibility with third-party kits. This section includes information on each Single Cell RNA Library Kit and the compatible third-party kit. For information on Illumina trademarks, see Legal Information and Guidelines.

Single Cell RNA Library Kits Compatibility

Single Cell Library Kit Types 1–5

The following image represents the genetic structure for Single Cell RNA Library Kit Types 1–5.

Single Cell RNA Library Prep Kits 1–5 are compatible with the following third-party kits.

Single Cell RNA Library Kit Type	Third-party Kit	Manufacturer
Single Cell RNA Library Kit 1	Chromium Next GEM Single Cell 3' v3.1	10x Genomics
Single Cell RNA Library Kit 1	Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (gene expression only)	10x Genomics
Single Cell RNA Library Kit 2	Chromium Single Cell 3' v2	10x Genomics
Single Cell RNA Library Kit 3	Chromium Single Cell 5' v1	10x Genomics
Single Cell RNA Library Kit 4	Chromium Next GEM Single Cell 5' v2 (Dual Index)	10x Genomics
Single Cell RNA Library Kit 5	Drop-seq	Dolomite

Single Cell Library Kit Type 6

The following image represents the genetic structure for Single Cell RNA Library Kit Type 6. Single Cell RNA Library Kit Type 6 is compatible with the BD Rhapsody Targeted mRNA and AbSeq Amplification, BD Biosciences.

Index Kit Compatibility

Single Cell RNA Library Prep Kits are compatible with the following index kits.

Single Cell RNA Library Kit Type	Index Adapters	Index Kit	Manufacturer
Single Cell RNA Library Kit 1	Single Cell RNA Index-Adapters 1	Single Index Kit T Set A	10x Genomics
Single Cell RNA Library Kit 1	Single Cell RNA Index-Adapters 1-B	Dual Index Kit TT Set A	10x Genomics
Single Cell RNA Library Kit 2	Single Cell RNA Index-Adapters 2	Chromium i7 Multiplex Kit	10x Genomics
Single Cell RNA Library Kit 3	Single Cell RNA Index-Adapters 3	Chromium i7 Multiplex Kit	10x Genomics
Single Cell RNA Library Kit 4	Single Cell RNA Index-Adapters 4-A	Dual Index Kit TN Set A	10x Genomics
Single Cell RNA Library Kit 4	Single Cell RNA Index-Adapters 4-B	Dual Index Kit TT Set A	10x Genomics
Single Cell RNA Library Kit 5	Single Cell RNA Index-Adapters 5	Nextera XT Indexes	Illumina
Single Cell RNA Library Kit 6	Single Cell RNA Index-Adapters 6	Library Reverse Primer 1-4	BD Biosciences

Single Cell ATAC Library Kit Compatibility

Single Cell ATAC Library Kit Types 1–2

The following image represents the genetic structure for Single Cell ATAC Library Kit 1.

The following image represents the genetic structure for Single Cell ATAC Library Kit 2

Single Cell ATAC Library Kits 1–2 are compatible with the following third-party kits.

Single Cell ATAC Library Kit Type

Third-party Kit

Manufacturer

Single Cell ATAC Library Kit 1

Chromium Next GEM Single Cell ATAC

10x Genomics

Single Cell ATAC Library Kit 2

Chromium Next GEM Single Cell Multiome ATAC + Gene Expression

(ATAC only)

10x Genomics

Index Kit Compatibility

Single Cell ATAC Library Prep Kits are compatible with the following index kits.

Single Cell ATAC Library Kit Type	Index Adapters	Index Kit	Manufacturer
Single Cell ATAC Library Kit 1	Single Cell ATAC Index-Adapters 1	Single Index Kit N Set A	10x Genomics
Single Cell ATAC Library Kit 2	Single Cell ATAC Index-Adapters 2	Single Index Kit N Set A	10x Genomics

Single Cell RNA Product Compatibility