Suppr超能文献

邻近连接杂交技术(PLISH)的进展。

Advances in Proximity Ligation Hybridization (PLISH).

作者信息

Nagendran Monica, Andruska Adam M, Harbury Pehr B, Desai Tushar J

机构信息

Department of Internal Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford, California, USA.

Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA.

出版信息

Bio Protoc. 2020 Nov 5;10(21):e3808. doi: 10.21769/BioProtoc.3808.

Abstract

Understanding tissues in the context of development, maintenance and disease requires determining the molecular profiles of individual cells within their native spatial context. We developed a Proximity Ligation Hybridization technology (PLISH) that enables quantitative measurement of single cell gene expression in intact tissues, which we have now updated. By recording spatial information for every profiled cell, PLISH enables retrospective mapping of distinct cell classes and inference of their interactions. PLISH has high sensitivity, specificity and signal to noise ratio. It is also rapid, scalable, and does not require expertise in molecular biology so it can be easily adopted by basic and clinical researchers.

摘要

要在发育、维持和疾病的背景下理解组织,需要在其原生空间背景中确定单个细胞的分子谱。我们开发了一种邻近连接杂交技术(PLISH),它能够对完整组织中的单细胞基因表达进行定量测量,我们现在已经对其进行了更新。通过记录每个被分析细胞的空间信息,PLISH能够对不同细胞类别进行回顾性映射,并推断它们之间的相互作用。PLISH具有高灵敏度、特异性和信噪比。它还快速、可扩展,并且不需要分子生物学方面的专业知识,因此基础研究人员和临床研究人员都可以轻松采用。

相似文献

1
Advances in Proximity Ligation Hybridization (PLISH).
Bio Protoc. 2020 Nov 5;10(21):e3808. doi: 10.21769/BioProtoc.3808.
3
Computational solutions for spatial transcriptomics.
Comput Struct Biotechnol J. 2022 Sep 1;20:4870-4884. doi: 10.1016/j.csbj.2022.08.043. eCollection 2022.
4
5
Mapping Cellular Coordinates through Advances in Spatial Transcriptomics Technology.
Mol Cells. 2020 Jul 31;43(7):591-599. doi: 10.14348/molcells.2020.0020.
6
Click chemistry-based amplification and detection of endogenous RNA and DNA molecules in situ using clampFISH probes.
Methods Enzymol. 2020;641:459-476. doi: 10.1016/bs.mie.2020.04.049. Epub 2020 Jun 15.
7
Protocol to assess RNA-RNA interactions in situ using an RNA-proximity ligation assay.
STAR Protoc. 2022 Dec 16;3(4):101892. doi: 10.1016/j.xpro.2022.101892. Epub 2022 Dec 1.
8
The "in situ" proximity ligation assay to probe protein-protein interactions in intact tissues.
Methods Mol Biol. 2014;1174:397-405. doi: 10.1007/978-1-4939-0944-5_27.
9
Lighting Up Nucleic Acid Modifications in Single Cells with DNA-Encoded Amplification.
Acc Chem Res. 2022 Aug 16;55(16):2248-2259. doi: 10.1021/acs.accounts.2c00269. Epub 2022 Jul 29.
10
Spatial Transcriptomics: Emerging Technologies in Tissue Gene Expression Profiling.
Anal Chem. 2023 Oct 24;95(42):15450-15460. doi: 10.1021/acs.analchem.3c02029. Epub 2023 Oct 10.

引用本文的文献

1
Evidence for lung barrier regeneration by differentiation prior to binucleated and stem cell division.
J Cell Biol. 2023 Dec 4;222(12). doi: 10.1083/jcb.202212088. Epub 2023 Oct 16.
2
KRAS(G12D) drives lepidic adenocarcinoma through stem-cell reprogramming.
Nature. 2023 Jul;619(7971):860-867. doi: 10.1038/s41586-023-06324-w. Epub 2023 Jul 19.
3
Cellular and molecular architecture of submucosal glands in wild-type and cystic fibrosis pigs.
Proc Natl Acad Sci U S A. 2022 Jan 25;119(4). doi: 10.1073/pnas.2119759119.

本文引用的文献

1
Cell Atlas technologies and insights into tissue architecture.
Biochem J. 2020 Apr 30;477(8):1427-1442. doi: 10.1042/BCJ20190341.
2
OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes.
Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2183-E2192. doi: 10.1073/pnas.1714530115. Epub 2018 Feb 20.
3
Single-cell Wnt signaling niches maintain stemness of alveolar type 2 cells.
Science. 2018 Mar 9;359(6380):1118-1123. doi: 10.1126/science.aam6603. Epub 2018 Feb 1.
5
The stacked-X DNA Holliday junction and protein recognition.
J Mol Recognit. 2006 May-Jun;19(3):234-242. doi: 10.1002/jmr.765.
6
Solution formation of Holliday junctions in inverted-repeat DNA sequences.
Biochemistry. 2006 Feb 28;45(8):2467-71. doi: 10.1021/bi052129x.
7
Stereospecific effects determine the structure of a four-way DNA junction.
Chem Biol. 2005 Feb;12(2):217-28. doi: 10.1016/j.chembiol.2004.12.006.
8
The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions.
Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):3971-6. doi: 10.1073/pnas.97.8.3971.
9
Crossover isomer bias is the primary sequence-dependent property of immobilized Holliday junctions.
Proc Natl Acad Sci U S A. 1997 Aug 19;94(17):9080-4. doi: 10.1073/pnas.94.17.9080.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验