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基准转录组解卷方法用于估计特定于组织和细胞类型的细胞外囊泡丰度.

Jannik Hjortshøj Larsen1, Iben Skov Jensen1, Per Svenningsen1

  • 1Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark.

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概括

准确估计组织和细胞类型特定的细胞外囊泡 (EV) 在体液中的丰度是具有挑战性的. 这项研究对解卷方法进行了基准测试,发现DWLS和CIBERSORTx对于EV RNA分析非常准确.

关键词:
细胞有条件介质的介质.外基因组是外基因组中的一个.微微的微小的微小的微小的微小的微小血等离子体是什么?一个单细胞RNA测序.转录组 (transcriptome) 是一个转录组.尿液 尿液 尿液

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科学领域:

  • 生物化学 生化学
  • 分子生物学分子生物学
  • 生物信息学是一种生物信息学.

背景情况:

  • 细胞外囊泡 (EVs) 携带重要的生物分子,但很难量化它们在生物流体中的组织和细胞类型特定来源.
  • 分析转录组的解卷方法对估计EV丰度有希望,但需要对EV数据进行性能评估.

研究的目的:

  • 为了对11种解卷方法的性能进行基准测试和比较,以估计人体生物流体中特定于组织和细胞类型的EV丰度.
  • 确定影响解卷精度的因素,并评估不同样本类型和隔离程序之间的方法一致性.

主要方法:

  • 评估了使用细胞系EVs,in silico混合物,人体血EVs (n=118) 和尿液EVs (n=88) 的11个解卷算法.
  • 评估方法的准确性,从纯和混合的EV样本中估计细胞类型特定的丰度.
  • 在两个尿液EV队列和评估的血EV估计中比较了四种解卷方法的结果.

主要成果:

  • 确定了对纯净和混合EV样品具有高精度的特定解卷方法.
  • 在尿液EVs的四种解卷方法中,无论分离技术如何,都显示出高度一致性.
  • 在血EV丰度估计的三种方法之间显示出强烈的一致性,并确定了准确性的关键因素.

结论:

  • 解卷算法DWLS和CIBERSORTx提供了组织和细胞类型特定的生物流体中EV丰度的准确和一致的估计.
  • 将生物知识纳入签名创建中对于提高解卷精度至关重要.
  • 这项工作验证了用于表征生物流体中的EV种群的解卷方法.