Slide-tags enables single-nucleus barcoding for multimodal spatial genomics.
Slide-tags enables single-nucleus barcoding for multimodal spatial genomics.
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DOI：
10.1038/s41586-023-06837-4
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发表时间：
2024-01
期刊：
影响因子：
64.8
通讯作者：
Chen, Fei
中科院分区：
文献类型：
--
作者：
Russell, Andrew J. C.;Weir, Jackson A.;Nadaf, Naeem M.;Shabet, Matthew;Kumar, Vipin;Kambhampati, Sandeep;Raichur, Ruth;Marrero, Giovanni J.;Liu, Sophia;Balderrama, Karol S.;Vanderburg, Charles R.;Shanmugam, Vignesh;Tian, Luyi;Iorgulescu, J. Bryan;Yoon, Charles H.;Wu, Catherine J.;Macosko, Evan Z.;Chen, Fei
最新的技术创新使基因表达和表观遗传调节的高通量定量转化了我们对复杂时机的理解，但是，这些测量值不足以常规地定位这些分析的细胞策略，幻灯片标签，其中完整组织中的单个核用空间条形码寡核苷酸标记衍生自具有已知位置的DNA-Barcoded珠子。与普通的单核RNA-Sere-Seporting数据质量无法区分的全转录组数据。人类组织的多样性，我们对大脑，扁桃体和黑色素瘤进行了评估。 - 标签是，它很容易适应几乎所有单细胞测量技术。来自转移性黑色素瘤的同一细胞中的T细胞受体（TCR）序列，鉴定转录因子在空间不同的微环境中驱动癌细胞态转变，提供了一个通用平台，用于进口已建立的单细胞测量值曲目。
幻灯片标签可以使单个细胞及其在组织中的定位进行多构测序。
Recent technological innovations have enabled the high-throughput quantification of gene expression and epigenetic regulation within individual cells, transforming our understanding of how complex tissues are constructed. However, missing from these measurements is the ability to routinely and easily spatially localize these profiled cells. We developed a strategy, Slide-tags, in which single nuclei within an intact tissue section are tagged with spatial barcode oligonucleotides derived from DNA-barcoded beads with known positions. These tagged nuclei can then be used as an input into a wide variety of single-nucleus profiling assays. Application of Slide-tags to the mouse hippocampus positioned nuclei at less than 10 μm spatial resolution and delivered whole-transcriptome data that are indistinguishable in quality from ordinary single-nucleus RNA-sequencing data. To demonstrate that Slide-tags can be applied to a wide variety of human tissues, we performed the assay on brain, tonsil and melanoma. We revealed cell-type-specific spatially varying gene expression across cortical layers and spatially contextualized receptor–ligand interactions driving B cell maturation in lymphoid tissue. A major benefit of Slide-tags is that it is easily adaptable to almost any single-cell measurement technology. As a proof of principle, we performed multiomic measurements of open chromatin, RNA and T cell receptor (TCR) sequences in the same cells from metastatic melanoma, identifying transcription factor motifs driving cancer cell state transitions in spatially distinct microenvironments. Slide-tags offers a universal platform for importing the compendium of established single-cell measurements into the spatial genomics repertoire. Slide-tags enables multiomic sequencing of single cells and their localization within tissues.
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影响因子：
46.9
作者：
Bolotin DA;Poslavsky S;Davydov AN;Frenkel FE;Fanchi L;Zolotareva OI;Hemmers S;Putintseva EV;Obraztsova AS;Shugay M;Ataullakhanov RI;Rudensky AY;Schumacher TN;Chudakov DM
通讯作者：
Chudakov DM
影响因子：
48
作者：
Biancalani T;Scalia G;Buffoni L;Avasthi R;Lu Z;Sanger A;Tokcan N;Vanderburg CR;Segerstolpe Å;Zhang M;Avraham-Davidi I;Vickovic S;Nitzan M;Ma S;Subramanian A;Lipinski M;Buenrostro J;Brown NB;Fanelli D;Zhuang X;Macosko EZ;Regev A
通讯作者：
Regev A
影响因子：
46.9
作者：
Clark, Iain C.;Fontanez, Kristina M.;Meltzer, Robert H.;Xue, Yi;Hayford, Corey;May-Zhang, Aaron;D'Amato, Chris;Osman, Ahmad;Zhang, Jesse Q.;Hettige, Pabodha;Ishibashi, Jacob S. A.;Delley, Cyrille L.;Weisgerber, Daniel W.;Replogle, Joseph M.;Jost, Marco;Phong, Kiet T.;Kennedy, Vanessa E.;Peretz, Cheryl A. C.;Kim, Esther A.;Song, Siyou;Karlon, William;Weissman, Jonathan S.;Smith, Catherine C.;Gartner, Zev J.;Abate, Adam R.
通讯作者：
Abate, Adam R.
DOI：
10.1073/pnas.0807297105
发表时间：
2008-09-30
影响因子：
11.1
作者：
Anderson, Ericka L.;Baltus, Andrew E.;Page, David C.
通讯作者：
Page, David C.
影响因子：
12.3
作者：
Choudhary S;Satija R
通讯作者：
Satija R