Maximize the Throughput and Cost–Efficiency of Your Single Cell Sequencing with the Max Read Kit on 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 paired reads when using the Max Read kit.

The Max Read Kit: Powerful Single Cell RNA Sequencing on 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 G4, generating 800 million paired 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.

Reagent Configuration1Run Time2Paired Reads / Flow Cell3Paired Reads / Run3Quality4
F2 Flow Cell 100 cycles~11 hours 200M 800M >80% bases
≥ Q30
200 cycles~15 hours
300 cycles~19 hours
F3 Flow Cell50 cycles~11 hours400M1.6B
100 cycles~14 hours
200 cycles~19 hours
300 cycles~24 hours
Max Read528x91 Single Cell~30 hours800M3.2B
28x50 Spatial FFPE~24 hours1.2B4.8B
  • 1 Reagents include 50 additional cycles above what is represented to account for index sequencing needs.
  • 2 Run time is measured from run start through clustering, sequencing, and instrument wash for non-indexed reads.
  • 3 Paired reads passing filter for F2 and F3 are approximates and dependent on application and read length.
  • 4 Performance metrics may be impacted by application, sample quality, library preparation, loading concentration, and other sequencing considerations. Metrics as generated on reference bacterial and human genomes.
  • 5 Currently only compatible with 10x Genomics Chromium™ 3′ and 5’ Gene Expression assays and Visium™ Spatial Gene Expression. Kits allow for 1 sample per lane.

Figure 1. The G4 Platform supports three throughput configurations: F2, F3, and Max Read. 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 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 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 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 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 Read)Flow Cell1 x M3
(800M paired reads)
2 x M3
(1.6B paired reads)
3 x M3
(2.4B paired reads)
4 x M3
(3.2B paired reads)
Price / Sample$200$200$200$200
Run Time (days)1111
NextSeq 20002Flow CellP3 100 cycle
(1.2B paired reads)
P3 + P2 100 cycle
(2 runs, 1.6B paired reads)
2x P3 100 cycle
(2 runs, 2.4B paired reads)
3x P3 100 cycle
(3 runs, 3.6B paired reads)
Price / Sample$832$598$555$624
Run Time (days)1223

1Assumes 10,000 cells and 20,000 paired 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
Single cell RNA sequencing preparation for Max Read sequencing begins with the a conventionally prepared scRNA-Seq library (Figure 3). The library is divided into three aliquots, each of which undergoes a PCR reaction to introduce sequences compatible with one of three unique sets of Max Read sequencing primers. The adapted libraries are combined, clustered at high density, then sequenced sequentially over three rounds, whereby each round utilizes one of the three sequencing primer pairs.

The Max Read Kit sequencing workflow

Figure 3. Max Read 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 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.

References
  1. Wen Lu, and Fuchou Tang. Recent advances in single-cell sequencing technologies. Precision Clinical Medicine. 5:1 Mar 2022. https://doi.org/10.1093/pcmedi/pbac002
  2. Van Wietmarschen, N. et al. “The Max Read® Kit for High-Throughput Single Cell Sequencing on the G4®.” Singular Genomics Systems, Inc. (2023) https://singulargenomics.com/max-reads/

Drew Spaventa

Drew founded Singular Genomics in 2016 serving as the CEO and Chairman. Drew is a serial entrepreneur and venture investor in the biotech industry and has been involved in the founding of several successful companies. Prior to Singular Genomics, Drew founded Truvian Sciences, a low volume blood testing technology aimed at making routine blood tests easier, less invasive, and more affordable. Drew was also involved in the founding of Aspen Neurosciences where he co-led the seed financing and helped assemble a world-class team to combat Parkinson’s Disease using a patient’s own stem cells. Drew was also a seed investor and held an operating role in Edico Genome which sold to Illumina in 2018.

Drew received an MBA from the Rady School of Management at the University of California, San Diego and a BA in Political Science and International Relations from the University of California, San Diego.

Max Reads Application Note