Probing In Vivo Structure of Individual mRNA 3' Isoforms Using Dimethyl Sulfate [0.03%]
利用二甲基硫酸盐探究单个mRNA 3'异构体的体内结构
Zarmik Moqtaderi,Joseph V Geisberg
Zarmik Moqtaderi
The DMS region extraction and deep sequencing (DREADS) procedure was designed to probe RNA structure in vivo and to link this structural information to specific 3' isoforms. Growing cells are treated with the alkylating agent dimethyl sulfa...
Generating Single Cell-Derived Knockout Clones in Mammalian Cells with CRISPR/Cas9 [0.03%]
在哺乳动物细胞中使用CRISPR/Cas9生成单倍体衍生的敲除克隆群
Christopher J Giuliano,Ann Lin,Vishruth Girish et al.
Christopher J Giuliano et al.
CRISPR/Cas9 technology enables the rapid generation of loss-of-function mutations in a targeted gene in mammalian cells. A single cell harboring those mutations can be used to establish a new cell line, thereby creating a CRISPR-induced kno...
STARR-seq and UMI-STARR-seq: Assessing Enhancer Activities for Genome-Wide-, High-, and Low-Complexity Candidate Libraries [0.03%]
STARR-seq和UMI-STARR-seq：评估全基因组范围内、高复杂度和低复杂度候选库中的增强子活性
Christoph Neumayr,Michaela Pagani,Alexander Stark et al.
Christoph Neumayr et al.
The identification of transcriptional enhancers and the quantitative assessment of enhancer activities is essential to understanding how regulatory information for gene expression is encoded in animal and human genomes. Further, it is key t...
Joseph V Geisberg,Zarmik Moqtaderi
Joseph V Geisberg
Here we describe CLIP-READS, a technique that combines elements of crosslinking and immunoprecipitation (CLIP) and 3' region extraction and deep sequencing (READS), to provide a genome-wide map of mRNA 3' isoform binding by a given messenge...
In Situ Hybridization for Detecting Mature MicroRNAs In Vivo at Single-Cell Resolution [0.03%]
单细胞分辨率下检测活体中成熟微小RNA的原位杂交方法
Amanda L Minogue,Swathi Arur
Amanda L Minogue
MicroRNAs (miRNAs) are key regulators of cell and tissue development. However, spatial resolution of miRNA heterogeneity and accumulation patterns in vivo remains uncharted. Next-generation sequencing methods assay miRNA abundance in tissue...
Digital Droplet PCR for Monitoring Tissue-Specific Cell Death Using DNA Methylation Patterns of Circulating Cell-Free DNA [0.03%]
基于游离DNA甲基化模式监测组织特异性细胞死亡的数字微滴PCR技术
Ruth Shemer,Judith Magenheim,Yuval Dor
Ruth Shemer
Cell death involves the release of short DNA fragments into blood, termed circulating cell-free DNA (cfDNA). Sequencing of cfDNA in the plasma has recently emerged as a liquid biopsy for detecting fetal chromosomal aberrations, tumor DNA, a...
Low-Input MNase Accessibility of Chromatin (Low-Input MACC) [0.03%]
低输入量MNase染色质可访问性分析(Low-Input MACC)
Mattia Lion,Michael Y Tolstorukov,Marjorie A Oettinger
Mattia Lion
An understanding of the dynamic structural properties of chromatin requires techniques that allow the profiling of regions of both open and closed chromatin as well as the assessment of nucleosome occupancy. The recently developed MNase acc...
Targeted Transcriptional Activation in Plants Using a Potent Dead Cas9-Derived Synthetic Gene Activator [0.03%]
利用高效的死Cas9衍生合成基因活化剂在植物中实现靶向转录激活
Zhenxiang Li,Fengzhu Wang,Jian-Feng Li
Zhenxiang Li
Genetic tools for specific perturbation of endogenous gene expression are highly desirable for interrogation of plant gene functions and improvement of crop traits. Synthetic transcriptional activators derived from the CRISPR/Cas9 system ar...
Fei Ji,Ruslan I Sadreyev
Fei Ji
Quantitative analysis of single-cell RNA sequencing (RNA-seq) is crucial for discovering the heterogeneity of cell populations and understanding the molecular mechanisms in different cells. In this unit we present a bioinformatics workflow ...
Transcriptome-Wide Mapping of m6 A and m6 Am at Single-Nucleotide Resolution Using miCLIP [0.03%]
利用miCLIP在单核苷酸分辨率对m6A和m6Am进行转录组范围的绘制
Ben R Hawley,Samie R Jaffrey
Ben R Hawley
The most prevalent modified base in mRNA, N6 -methyladenosine (m6 A), is found in several thousand transcripts, typically near the stop codon, although it can occur anywhere in the mRNA. In addition, the highly similar nucleotide N6 ,2'-O-d...