通过立体序列对物种不可知转录组进行全面的空间分析
Anna K Casasent1, Danielle L Stolley1, Basant T Gamal2
1Department of Hematopoietic Biology and Malignancies, The University of Texas MD Anderson Cancer Center.
Journal of visualized experiments : JoVE
|November 17, 2025
概括
这项研究引入了一种新的空间物种不可知立体次序协议,用于甲固定嵌 (FFPE) 组织. 它可以在它们的空间环境中检测各种RNA物种的细胞下分辨率,包括微生物和病毒RNA.
科学领域:
- 空间转录组学 空间转录组学
- 分子生物学分子生物学
- 基因组学就是基因组学.
背景情况:
- 细胞的空间组成和微生物负荷影响宿主组织相互作用.
- 现有的空间转录组学方法经常错过非传递 RNA (mRNA) 物种,如长非编码 RNA,线粒体 RNA 和微生物 RNA.
- 嵌入式甲固化 (FFPE) 组织对于全面的空间RNA分析具有价值,但具有挑战性.
研究的目的:
- 介绍FFPE组织上的空间物种不可知立体序列的详细协议.
- 为了能够检测广泛的RNA物种,包括宿主和非宿主RNA,具有亚细胞分辨率.
- 提供关于不同RNA分子在组织内的空间分布的见解.
主要方法:
- 使用随机启动方法与空间条形码用于在FFPE组织中捕获RNA.
- 采用随机探测方法来进行物种无关的RNA检测.
- 包含在样本处理过程中将内源RNA与环境污染物区分开来的具体考虑.
主要成果:
- 实现亚细胞分辨率 (0.22微米珠,0.5微米阵列) 用于空间RNA检测.
- 在FFPE组织中成功检测宿主和非宿主RNA (微生物,病毒).
- 提供多种RNA物种的高分辨率空间映射,包括单细胞级分辨率.
结论:
- 开发的空间立体测序协议与FFPE组织兼容,并提供广泛的RNA物种检测.
- 这种方法增强了对空间背景下的宿主-微生物和宿主-病原体相互作用的理解.
- 它为研究复杂组织微环境和疾病病理学提供了巨大的潜力.
相关概念视频
03:21RNA-seq
11.7K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
11.7K
02:24Ribosome Profiling
4.0K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
4.0K
02:51Multi-species Conserved Sequences
4.6K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.6K