![]() In total, five samples were sequenced: passages 2, 6, 7, and 8 through CCL81 cells and passage 2 through MRC5 cells. In addition, the sequence reads were de novo assembled using CLC bio. KC776147.1) using the CLC bio Genomics Workbench (version 6.5). Concerning genome engineering approaches based on nuclease-induced DNA double-strand breaks, this protocol could aid in detecting the unwanted effects caused by the donor fragments themselves. The reads were aligned against the NCBI reference (accession no. This work should pave the way for future genotoxicity analyses. Additionally, we demonstrated the usefulness of this approach for primary cells by treating human CD34 + hematopoietic stem and progenitor cells with a 100-nucleotide-long unmodified oligodeoxynucleotide directed against the endogenous CYBB locus. with the aim of producing longer sequences representative of genomic. onto the testis transcriptome using CLC Genomics Workbench respectively. For a 21-nucleotide-long phosphorothioate-modified oligodeoxynucleotide, we compiled a broad array of error-free incorporations, point mutations, indels, and structural rearrangements from actively dividing HEK293-derived cells. generation sequencing (NGS) data across the National Reference Laboratories (NRLs). How do I generate a de novo transcriptome reference usisng CLC Genomics Workbench I have a transcriptome sequenced data of B. PMC, Male-biased genes in catfish as revealed by RNA-Seq analysis of the testis. The reads were aligned to the reference haploid human genome sequence (Genome Reference Consortium human genome build 37, human genome 19 (hg19)). This protocol was validated in gene repair experiments without intentionally inducing a DNA double-strand break. Following sequencing, paired FASTQ files were generated using Illumina CASAVA-1.8.2 software and imported into CLC Genomics Workbench (Qiagen, Germany) for further processing. Affected chromosomal fragments are enriched and preferably sequenced by nanopore sequencing. Thus, we have developed a protocol that follows the fate of a biotin-labeled single-stranded oligodeoxynucleotide in human cells based on its physical incorporation into the targeted genome. Because the usability of single-stranded oligodeoxynucleotides depends on their efficiencies, as well as their specificities, analyzing their genotoxic off-target activities is important. They enable gene repair and genome editing, and they are central to the antisense technology. Short single-stranded oligodeoxynucleotides are versatile molecular tools used in different applications.
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