10x Genomics produces a family of sequencing-based assays for single-cell and spatial transcriptomics. All libraries are built on standard Illumina adapter chemistry (P5/P7, TruSeq primers), but differ in how cell or spatial barcodes and UMIs are introduced. The pages below document adapter sequences, step-by-step library generation, and sequencing workflows for each assay.
Chromium Single Cell
Chromium Fixed RNA Profiling (Flex)
Probe-based gene expression for fixed (FFPE/methanol) samples. Probe pairs hybridise to mRNA; ligation creates the sequencing template.
scRNA-seq · 5′Chromium Single Cell 5′ GE
Droplet-based 5′ gene expression and V(D)J profiling. Barcoded TSO on gel beads captures the 5′ end of transcripts.
scRNA-seq · 3′Chromium Single Cell 3′ GE
Droplet-based 3′ gene expression. Barcoded oligo-dT beads capture polyadenylated mRNA inside GEMs.
Visium Spatial Gene Expression
Visium HD 3′
High-definition spatial at 2 µm bin resolution. Whole-transcriptome 3′ poly-T capture (no probes). Expanded species compatibility.
Spatial HD · ProbeVisium HD WT Panel
High-definition spatial at 2 µm bin resolution. Whole-transcriptome panel (probe-based). Requires CytAssist. FFPE, FF, fixed-frozen.
Spatial · ProbeVisium v2 (WT Panel)
CytAssist-enabled probe-based Visium. Compatible with FFPE, fresh-frozen, and fixed-frozen tissues. Requires CytAssist instrument.
Spatial · 3′ FFVisium v1
First-generation Visium. 55 µm capture spots on a slide capture polyadenylated mRNA via poly-T probes. Fresh-frozen tissue only.