Maximize the Throughput and Cost–Efficiency of Your Single Cell Sequencing with the Max Read™ Kit on the G4™

May 31, 2023

Are you batching your single cell transcriptome experiments to fill a high-capacity flow cell for more cost-effective sequencing, but at the expense of adding weeks to your timelines?

Meet the high-throughput, low-cost Max Read Kit.

Single cell RNA sequencing (scRNA-Seq) provides important information on cellular function and diversity that is critical to advancing precision medicine, but due to high costs this technique is challenging to implement for many laboratories. Since 2009, advances in scRNA-Seq have been limited to improvements in single cell sorting and library preparation rather than making the technology high-throughput and cost-efficient. Most traditional benchtop sequencers, remain expensive to operate, and have long turnaround times.

The G4™ Sequencing Platform however, delivers fast, flexible sequencing and will deliver 3.2 billion reads per run at a cost of only $1 per million reads when using the Max Read™ Kit.

The Max Read Kit: Powerful Single Cell RNA Sequencing on the G4
The Max Read Kit is designed to maximize throughput and cost-efficiency of scRNA-Seq on the G4 Sequencing Platform. It contains all components necessary to prepare and sequence compatible 10x Genomics® libraries on the G4, including materials for sample preparation and loading, flow cell, reagent cartridge, and Max Read PhiX Control.

Maximize Throughput
The Max Read Kit maximizes scRNA-Seq throughput on the G4, generating 800 million reads per flow cell and 3.2 billion reads across 4 flow cells in a single 24-hour run (Figure 1). By processing 16 samples per day, 5 days per week, laboratories can sequence up to 80 samples per week and 4,160 single cell samples per year for unmatched throughput.

F2 Flow CellF3 Flow CellMax Reads1
Reads Delivered / Flow Cell~200 M2~400 M2~800 M
Reads Delivered / Run~800 M2~1,600 M2~3,200 M
# Samples / Flow Cell3124
# Samples / Run34816
Price/M Read~$3.0~$1.8$1.0
Run Time11-14 hours411-14 hours4~24 hours4
Quality (%Q30)80-90%80-90%80-90%

Numbers are projected and results may vary. Refer to kit specifications for more detail.
1Max Read kits specifications are projected, and kits are currently only compatible with 10x Genomics ChromiumTM 3 and 5’ Gene Expression assays and VisiumTM Spatial Gene Expression. Kits allow for 1 sample per lane
2Throughputs listed are approximations and not guaranteed above kit specifications. Results may vary based on experimental design and sample type.
3Assumes 28×91 read configuration, 10,000 cells/sample and 20,000 reads/cell
4Run time includes clustering, sequencing and instrument wash for non-indexed reads

Figure 1. The G4 Platform supports three throughput configurations: F2, F3, Max Reads. This flexibility enables efficient experimental design, rapid turnaround time, and low costs per sample.

Cost-Efficient Sequencing Within One Day
Traditional sequencing platforms utilize high-capacity flow cells with limited flexibility. As a result, laboratories often batch samples to fill flow cells prior to each instrument run in an effort to make sequencing more cost-efficient. However, this practice can result in long turnaround times to generate data. Alternatively, labs may proceed with partially filled flow cells to meet rapid turnaround times resulting in wasted capacity, wasted reagents, and higher costs per sample sequenced. These operational challenges are easily resolved with the G4, and with the Max Read Kit, laboratories get unmatched scRNA-Seq throughput and cost-efficiency.

A comparison of the costs and turnaround for samples processed using the Max Read Kit on the G4, to samples processed on the Illumina NextSeq® 2000 is shown in Figure 2.

To run just 4 samples on the NextSeq 2000 system with its high-capacity flow cells, laboratories will spend nearly $800+ per sample, but on the G4 (Max Read), labs can run 4, 8, 12, or 16 samples for only $200 per sample. The $200 per sample cost consistency on the G4 is achieved by tailoring the flow cell capacity to a given sample set, thereby reducing costs associated with reagent waste.

Although 4 samples can be turned around in one day on the NextSeq 2000, larger sets of 8-16 samples require 2-3 days turnaround and multiple runs. With Max Read on the G4, labs can sequence from 1 to 16 samples in parallel in a single day—no more batching and waiting for results.

4 Samples8 Samples12 Samples16 Samples
G4 (Max Reads)Flow Cell used1 x M3
(800M reads)
2 x M3
(1,600M reads)
3 x M3
(2,400M reads)
4 x M3
(3,200M reads)
Price / Sample$200$200$200$200
Run Time (days)1111
NextSeq 2000Flow Cell usedP3 100 cycle
(1,200M reads)
P3 + P2 100 cycle
(2 Runs, 1,600M reads)
2x P3 100 cycle
(2runs, 2,400M reads)
3x P3 100 cycle
(3 runs, 3,600M reads)
Price / Sample$832$598$555$624
Run Time (days)1223

1Assumes 10,000 cells and 20,000 reads
2Reflects publicly available list prices

Figure 2. Sample throughput, costs per sample, and turnaround times are compared for the G4 (Max Read Kit) and the Illumina NextSeq® 2000.

How the Max Read Kit Works
Sequencing using the Max Read Kit begins with the preparation of a scRNA-Seq library using conventional library preparation methods (Figure 3). The library is divided into three aliquots, each of which is PCR-converted to introduce sequences compatible with one of three unique sets of sequencing primers. Converted libraries are re-pooled and clustered at high density on a patterned flow cell to produce a plurality of polyclonal clusters. Clusters are deciphered over 3 successive rounds of sequencing, with each round using one of three sets of sequencing primers. Each polyclonal cluster will give rise to multiple high-quality reads, thereby maximizing the capacity of the flow cell.

The Max Read Kit sequencing workflow

Figure 3. The Max Read Kit sequencing workflow.

Highly Accurate Single Cell Sequencing
While the Max Read Kit is built for high throughput, rapid turnaround, and cost-efficiency, it also delivers highly accurate scRNA-Seq results that are concordant with industry standard sequencing. To demonstrate this, we prepared a library using the 10x Genomics 3’ RNA-Seq kit, split the library, and sequenced portions on the NextSeq 2000 and the G4 (Max Read). Results from each sequencer were compared and showed a high degree of correlation, identical UMAP clustering, and near-identical gene expression of immune cell markers. For additional data on the performance of the Max Read Kit, download our poster.

Achieve higher throughput and faster turnaround of your scRNA-Seq experiments with the Max Read Kit on the G4 Sequencing Platform. The unique flexibility of the G4 paired with the Max Read workflow delivers cost-efficient sequencing that will enable more laboratories to utilize single cell technology to improve our understanding of complex biological systems.

Learn more about the Max Read Kit and how it can maximize your sequencing efficiency.

  1. Wen Lu, and Fuchou Tang. Recent advances in single-cell sequencing technologies. Precision Clinical Medicine.5:1  Mar 2022.
  2. Van Weitmarschen, N. et al. “The Max Read™ Kit for High-Throughput Single Cell Sequencing on the G4™.” Singular Genomics Systems, Inc. (2023)

Max Reads Application Note