Question: Can I detect alternative transcript isoforms using 10x assays?
Answer: Yes, combining long-read sequencing with 10x assays enables the unambiguous identification of alternative splicing at single cell resolution. Unique isoforms associated with specific cell types can be distinguished which are otherwise undetectable using short-read single-cell RNA-Seq. While these workflows are customer enabled using workflows from 10x Compatible Partners Oxford Nanopore Technologies (ONT) or Pacific Biosciences (PacBio), they are unsupported by 10x Genomics since they require workflow modifications and additional 3rd party reagents.
Summary of compatibility of long-read sequencing platforms with 10x Assays:
| 10x Assay |
10x Compatible Partners* |
|
|
Oxford Nanopore Technologies (ONT): PromethION™ Sequencing Devices |
Pacific BioSciences (PacBio): MAS-Seq for 10x Single Cell 3’ kit |
|
|
Single Cell Gene Expression (i.e., 3’ v3.1) |
3' GEX: Compatible 3’ v3.1 LT or HT: Not tested |
3' GEX: Compatible 3’ v3.1 LT or HT: Not tested |
|
Single Cell Immune Profiling (i.e., 5’ v2) |
5’ GEX: Compatible 5’ V(D)J: Incompatible 5’ GEX HT: Not tested |
5’ GEX: Compatible but currently unsupported* 5’ V(D)J: Incompatible 5’ GEX HT: Not tested |
|
ATAC |
Incompatible |
Incompatible |
|
Multiome ATAC + GEX |
3’ GEX: Compatible ATAC: Incompatible |
3’ GEX: Compatible ATAC: Incompatible |
|
Fixed RNA Profiling |
Incompatible |
Incompatible |
|
Spatial Gene Expression (i.e., Visium for Fresh Frozen Tissues) |
Compatible |
Compatible but currently unsupported* |
|
Spatial Gene Expression for FFPE (i.e., Visium for FFPE Tissues) |
Incompatible |
Incompatible |
*Please reach out directly to PacBio or ONT for additional information regarding compatibility of 10x assays with long-read sequencing.
The workflow modifications required for long-read sequencing are NOT expected to be compatible and unsupported with ATAC, 5' V(D)J, Feature Barcode, Fixed RNA Profiling or Visium for FFPE workflows.
For additional information including 3rd party reagents and workflow modifications required, please see: Which 10x Assays are compatible with long-read sequencing applications?
Products:
Single Cell Gene Expression, Single Cell Immune Profiling, Single Cell Multiome ATAC+GEX, Spatial Gene Expression for Fresh Frozen.