High-depth spatial transcriptome analysis by photo-isolation chemistry.
High-depth spatial transcriptome analysis by photo-isolation chemistry.
复制标题
DOI：
10.1038/s41467-021-24691-8
复制
发表时间：
2021-07-20
影响因子：
16.6
通讯作者：
Ohkawa Y
中科院分区：
文献类型：
--
作者：
Honda M;Oki S;Kimura R;Harada A;Maehara K;Tanaka K;Meno C;Ohkawa Y
在多细胞生物体中，空间限定区域的表达谱对于阐明细胞相互作用和功能至关重要。在这里，我们建立了一个转录组分析方法加上光隔离化学（PIC），允许确定表达谱，特别是从光照射的区域的利益。PIC使用光笼寡脱氧核苷酸进行原位逆转录。PIC转录组分析检测在小鼠胚胎的小的不同区域中特异性表达的基因。单细胞的光照射表明，检测到约8，000个基因，具有7 × 104个独特读段计数。此外，PIC转录组分析适用于亚细胞和亚核微结构（分别为应力颗粒和核斑点），其中可以检测到数百个基因被特异性定位。读段计数的空间密度高于每平方微米100个。因此，PIC能够从有限的区域直到亚细胞和亚核分辨率来确定高深度的转录组谱。RNAseq数据的空间分析非常重要。在这里，作者报告了一种转录组分析结合光隔离化学的方法，以确定他们在小鼠大脑和胚胎组织中使用的特定光照射区域的表达谱。
In multicellular organisms, expression profiling in spatially defined regions is crucial to elucidate cell interactions and functions. Here, we establish a transcriptome profiling method coupled with photo-isolation chemistry (PIC) that allows the determination of expression profiles specifically from photo-irradiated regions of interest. PIC uses photo-caged oligodeoxynucleotides for in situ reverse transcription. PIC transcriptome analysis detects genes specifically expressed in small distinct areas of the mouse embryo. Photo-irradiation of single cells demonstrated that approximately 8,000 genes were detected with 7 × 104 unique read counts. Furthermore, PIC transcriptome analysis is applicable to the subcellular and subnuclear microstructures (stress granules and nuclear speckles, respectively), where hundreds of genes can be detected as being specifically localised. The spatial density of the read counts is higher than 100 per square micrometre. Thus, PIC enables high-depth transcriptome profiles to be determined from limited regions up to subcellular and subnuclear resolutions. Spatial analysis of RNAseq data is important. Here the authors report a method for transcriptome profiling combined with photo-isolation chemistry to allow determination of expression profiles specifically from photo-irradiated regions of interest which they use in mouse brains and embryonic tissues.
登录
查看更多内容
影响因子：
16.6
作者：
Hayashi T;Ozaki H;Sasagawa Y;Umeda M;Danno H;Nikaido I
通讯作者：
Nikaido I
影响因子：
46.9
作者：
Merritt, Christopher R.;Ong, Giang T.;Beechem, Joseph M.
通讯作者：
Beechem, Joseph M.
影响因子：
14.8
作者：
Islam, Saiful;Kjallquist, Una;Linnarsson, Sten
通讯作者：
Linnarsson, Sten
影响因子：
4.7
作者：
Kuzuya, Akinori;Okada, Fuminori;Komiyama, Makoto
通讯作者：
Komiyama, Makoto
影响因子：
56.9
作者：
Femino, A;Fay, FS;Singer, RH
通讯作者：
Singer, RH