RNA was extracted and used for preparation of cDNA libraries, which were sequenced by the Delaware Biotechnology Institute (DBI) using HiSeq2500. Sequence reads were aligned to the chicken reference genome with HISAT, and genes were analyzed for differential expression between regions of the breast ...
本文首发于公众号“bioinfomics”:Seurat包学习笔记(三):Analysis of spatial datasets 本次教程中,我们将学习如何使用Seurat3处理空间转录组数据。整体的分析流程类似于Seurat的单细胞RNA-seq分析流程,同时…
[1] Yan L, Yang M, Guo H, et al. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol 2013, 20(9):1131-9. [2] Xi C, Teichmann SA, Meyer KB. From Tissues to Cell Types and Back: Single-Cell Gene Expression Analysis of Tiss...
Spatial transcriptomics technologies with high resolution often lack high sensitivity in mRNA detection. Here we report a dendrimeric DNA coordinate barcoding design for spatial RNA sequencing (Decoder-seq), which offers both high sensitivity and high re
在大多数情况下,但不是全部情况下,细胞间通讯需要细胞靠得很近才能通过配体-受体相互作用交换信号。然而,单细胞 RNAseq 数据在组织制备过程中会丢失这些信息。在本笔记本中,我们将学习如何在 Cellphone BD 版…
在人类乳腺肿瘤中发现了衰老乳腺细胞的转录特征,这表明衰老与癌症之间可能存在联系。 年龄是癌症的最大危险因素,三分之二的癌症发生在50岁以上的女性 表观遗传学的变化是衰老的标志,可以作为转录和细胞特性与年龄相关变化的分子驱动因素。 结果1、乳腺随着年龄的增长而发生细胞组成变化 ...
Reconstructing gene-gene co-expression networks is a common analysis performed with non-spatial single cell RNA-seq data46. To test if the global d-colocalization map reflects such co-expression networks or if it reveals a different type of relationship, we derived a co-expression network from ...
We offer spatial profiling utilizing the 10X Genomics® Visium HD® platform. This novel technology performs simultaneous,in situspatial analysis from a single FFPE or frozen tissue section. You can select from a host of discovery-focused panels with the potential for customization. Together with...
et al. Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling. Nat. Methods 16, 1007–1015 (2019). Article CAS PubMed PubMed Central Google Scholar Levine, J. H. et al. Data-driven phenotypic dissection of AML reveals progenitor-like cells that ...
而scRNA-seq技术的检测效率在3%到25%之间,Cartana ISS和FISSEQ的检测效率分别为~5%和~0.005%,STARmap只比scRNA-seq好一点。然而,与smFISH相比,ExSeq表示每个细胞的检测基因的效率高达62%。较新的技术倾向于跳过RT,使挂锁探针在RNA模板上的连接更有效,如BOLORAMIS和基于杂交的RNA ISS(HybRISS),或者用类似seqFISH...