To perform ultra-deep sequencing of tumor suppressors and oncogenes, we used a hybrid-capture NGS assay for detection of DNA variants at high depth across the exons of 523 cancer-relevant genes (spanning 1.94 Mb of DNA) using unique molecular indexes (leveraging the TruSight Oncology 500 ...
PCa genetic risk SNPs are enriched in noncoding CREs rather than in protein-coding regions9,80. It is challenging to systematically evaluate the importance of these rCREs in cancer biology and the clinic. Our study demonstrates that CRISPRi mediated loss-of-function screen of rCREs is an effic...
CRISPR has proved to be a compelling tool for functional genomics, as it enables researchers to associate changes in phenotypes with highly specific knockouts. CRISPR-mediated loss-of-function screens are now commonplace for elucidating drug targets for therapeutic development. Two screen types- pooled...
MAGeCKFlute is distinguished from other currently available tools by its comprehensive pipeline, which contains a series of functions for analyzing CRISPR screen data. This protocol explains how to use MAGeCKFlute to perform quality control (QC), normalization, batch effect removal, copy-number bias ...
Calu-3 cells stably expressing Cas9 for the LOF screen or dCas9 and transcriptional activators for the GOF screen were transduced with pooled guide RNA libraries. Following infection with SARS-CoV-2, cells were harvested after at least 70% CPE was evident. Next-generation sequencing was ...
The cellular processes that govern tumor resistance to immunotherapy remain poorly understood. To gain insight into these processes, here we perform a genome-scale CRISPR activation screen for genes that enable human melanoma cells to evade cytotoxic T c
CROP-seq enables pooled CRISPR screens for complex transcriptome signatures by making gRNA expression detectable in single-cell RNA sequencing. CRISPR-based genetic screens are accelerating biological discovery, but current methods have inherent limitati
Direct-seq: employing programmed gRNA scaffold for streamlined scRNA-seq in CRISPR screen 来自 Semantic Scholar 喜欢 0 阅读量: 67 作者:L Wang,L Ma 摘要: This protocol aimed to combine the single cell RNA-seq (scRNA-seq) with the CRISPR screening assay based on 10x 3' RNA-seq platform to...
CRISPR screens in the field of virology are ideally suited for analyzing virus-host interactions; determining host factors critical for virus entry, replication, and spread; and identifying and prioritizing novel drug targets. Performing a genome-scale CRISPR/Cas9 knockout screen with an sgRNA library...
The sequencing libraries were quantified using qPCR with the KAPA Library Quantification Kit Illumina (KAPA Biosystems) for multiplexing. The multiplexed libraries were quantified using the same qPCR protocol and sequenced with 30–40% PhiX control using Illumina HiSeq2500 (HiSeq Rapid SBS kit; 2 x...