Single Cell ATAC Pre-Indexing Kit

With the ScaleBioTM Single Cell ATAC Pre-Indexing Kit, process 300,000 nuclei per run with a significant cost reduction while maintaining high data quality.


The ScaleBio Single Cell ATAC Pre-Indexing Kit enables the high-throughput processing of up to 300,000 nuclei per run using combinatorial indexing.
The upfront barcoding of isolated nuclei during tagmentation enables the superloading of existing droplet systems, enabling a 10-fold increase in throughput at a significant reduction in cost, without compromising on data quality.



300,000 nuclei per run

Recommended input

~50,000 nuclei/well (x24 wells)

Instrument compatibility

On-market single-cell droplet capture systems, such as the 10X Chromium controller

Schematic of the split-pool scheme for ScaleBio's Single Cell ATAC-Seq Kit

Single Cell ATAC Pre-Indexing Kit

This schematic shows an overview of the split-pool scheme for Single Cell ATAC Pre-Indexing Kit using ScaleBio. Nuclei are indexed during tagmentation and superloaded onto a droplet system, where an additional barcode is incorporated.

Single Cell ATAC Pre-Indexing Kit

The workflow is 1.5 hours with only 30 minutes of additional hands-on time, and enables superloading of on-market droplet systems.

Sample loading workflow for ScaleBio's Single Cell ATAC-Seq Kit

Frequently asked questions

We provide a total of 24 indexes in our kit, which are incorporated during tagmentation. We typically recommend to load between 20,000-50,000 nuclei per well. You can run up to 24 samples (50,000 nuclei/sample), or, for more nuclei per sample, run fewer samples across the plate.

We do provide a demultiplexing software which can be used directly on the raw data files obtained from Illumina’s sequencers.

We have tested compatibility on MiSeq, iSeq, NextSeq 500/550, NextSeq 1000/2000, NovaSeq6000.

Even with a 10-fold increase in throughput, our combinatorial indexing method results in an effective doublet rate of ~4.7%.

In our protocol, we describe the use of the Single Cell ATAC Pre-Indexing Kit upstream of the Chromium Next GEM Single Cell ATAC Reagent Kit (1000175/1000176).

Single Cell ATAC Pre-Indexing Kit resources


Want to learn more?


Featured publications View All

High content single-cell combinatorial indexing.

Nature Biotechnol. July 2021.


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