Thus, there is need for a new sequencing approach that is both rapid and cost-effective, yet offers robust assemblies suitable for genome-editing applications. Linked read technology (or read clouds) has the potential to fill this application gap by combining aspects of short and long reads via...
In this work, by combining the CRISPR-based enrichment with 10x Genomics linked-read sequencing and the PacBio HiFi long-read platform (Fig.1a), we were able to achieve targeted haplotype-resolved assembly of the MHC region from diploid human cells. We also applied our targeted approach to tw...
To try to understand this difference and to confirm that the II1 transgene was inserted at the expected position, we performed long-read sequencing with the Oxford Nanopore MinION in conjunction with the nCATS protocol29to enrich for sequencing reads covering the region around the insertion site (...
Circulating tumor DNA ELISA: Enzyme-linked immunosorbent assay FNA: Fine needle aspiration gDNA: Genomic DNA NSG: Next-generation sequencing PBL: Peripheral blood leukocyte SD: Standard deviation SNP: Single nucleotide polymorphism SNV: Single nucleotide variant ...
The created FASTQ file containing the raw read data, was uploaded to the publicly available online GALAXY suite of software for NGS data analysis (https://galaxyproject.org) [64], where the HISAT2 algorithm was used for the alignment of the obtained sequencing reads against the human reference...
As the image analysis work flow captures tumor cells as individual image objects, it leverages subsequent analyses in which the comprehensive information on local differences in HER2 ECD loss could be linked to other parameters of interest (eg, regional activation of HER2-associated oncogenic signaling...
Fusion genes are a major cause of cancer. Their rapid and accurate diagnosis can inform clinical action, but current molecular diagnostic assays are restricted in resolution and throughput. Here, we show that targeted RNA sequencing (RNAseq) can overcome
sequencing read counts are shown to the right of each site. GUIDE-seq sequencing read counts are shown to the right of each site.cTargeted high-throughput sequencing of off-target sites in edited (RNP) or electroporated-only (Mock) HSPCs (n = 2 experiments from two different donors;...
Next-generation sequencing 2D: 2 Dimensional 3D: 3 Dimensional MD: Molecular docking MDS: Molecular dynamics simulation QSAR: Quantitative structure–activity relationship VEGF: Vascular endothelial growth factor CLL: Chronic Lymphocytic Leukemia MUC1: Mucin 1 HER2: Human epidermal growth fac...
TNF-α tumor necrosis factor-alpha, Foxp3 forkhead box protein 3.cTumor occurrence and progression are closely linked to TME. Overactivation of NF-κB signaling not only promotes tumor cell survival, invasion, metastasis, genomic instability, and metabolic abnormalities, but also reshapes the immune...