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Leveraging Two Novel Droplet-Based Single-Cell RNA Sequencing Platforms: a Comparative Study With 10x Genomics

GSE300217 Homo sapiens; Mus musculus Expression profiling by high throughput sequencing 9 samples Submitted 2025/11/17 Platform GPL35959Platform GPL35109Platform GPL24676
Summary
Here we performed a comparison of two droplet-based high-throughput single-cell platforms, namely, SeekOne and MobiDrop with a widely-used commercial platform from 10x Genomics. The use of different types of samples allowed us to evaluate the performance of the platforms on cell suspensions of varying complexity and quality. 10x showed generally superior performance, although all platforms compared in this study showed acceptable gene yield and allowed identification of all expected cell types. Taking into account the cost and availability of devices and reagents required for each platform and the flexibility in the number of samples loaded onto the chip, SeekOne and MobiDrop might serve as a good alternative. The results of the current comparison will support the community's efforts to compare different aspects, including sample amount requirements, throughput, cell quality, gene capture efficiency and cell type representativeness.
Published in
Leveraging two novel droplet-based single-cell RNA Sequencing platforms: a comparative study with 10x genomics
Maluchenko AV, Avsievich ES, Zvorygina IS et al. · BMC genomics 2025 · PMID 41327014 · doi:10.1186/s12864-025-12355-6
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Direct links to NCBI, no account and no request form: the whole study as GSE300217_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 9 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA1279856 and SRA study SRP593306. Searching any of these in the dataset finder brings you back here.

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