Comparative transcriptomic analyses of thymocytes using 10x Genomics and Parse scRNA-seq technologies.

IF 3.5 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

BMC Genomics Pub Date : 2024-11-11 DOI:10.1186/s12864-024-10976-x

Igor Filippov, Chinna Susan Philip, Leif Schauser, Pärt Peterson

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引用次数: 0

Abstract

Background: Single-cell RNA sequencing experiments commonly use 10x Genomics (10x) kits due to their high-throughput capacity and standardized protocols. Recently, Parse Biosciences (Parse) introduced an alternative technology that uses multiple in-situ barcoding rounds within standard 96-well plates. Parse enables the analysis of more cells from multiple samples in a single run without the need for additional reagents or specialized microfluidics equipment. To evaluate the performance of both platforms, we conducted a benchmark study using biological and technical replicates of mouse thymus as a complex immune tissue.

Results: We found that Parse detected nearly twice the number of genes compared to 10x, with each platform detecting a distinct set of genes. The comparison of multiplexed samples generated from 10x and Parse techniques showed 10x data to have lower technical variability and more precise annotation of biological states in the thymus compared to Parse.

Conclusion: Our results provide a comprehensive comparison of the suitability of both single-cell platforms for immunological studies.

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利用 10x Genomics 和 Parse scRNA-seq 技术对胸腺细胞进行转录组比较分析。

背景：单细胞 RNA 测序实验通常使用 10x Genomics（10x）试剂盒，因为它们具有高通量能力和标准化方案。最近，Parse Biosciences（Parse）推出了一种替代技术，在标准 96 孔板中使用多轮原位条形码。Parse 可在一次运行中分析来自多个样本的更多细胞，而无需额外的试剂或专门的微流体设备。为了评估这两种平台的性能，我们使用作为复杂免疫组织的小鼠胸腺的生物和技术重复样本进行了一项基准研究：结果：我们发现 Parse 检测到的基因数量几乎是 10x 的两倍，每个平台都能检测到一组不同的基因。对 10x 和 Parse 技术产生的多重样本进行比较后发现，10x 数据与 Parse 相比，技术变异性更低，对胸腺生物状态的注释更精确：我们的研究结果全面比较了两种单细胞平台在免疫学研究中的适用性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

BMC Genomics 生物-生物工程与应用微生物

CiteScore

7.40

自引率

4.50%

发文量

769

审稿时长

6.4 months

期刊介绍： BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.