TDP1 gene knockout effect on transcriptome

TDP1 is an enzyme that in humans is encoded by the TDP1 gene.[5][6][7] TDP1 is the protein involved in repairing stalled topoisomerase I-DNA complexes. We evaluated the effect of Tdp1 knockout in HEK293A cells on the gene expression. Knockout HEK293A cell line was generated using the CRISPR/Cas9 method. gRNA were designed against region with constitutive protein-encoding exons of Tdp1 gene. Then, we performed comparative gene expression profiling analysis of RNA-seq data for HEK293A wild type cells and Tdp1-KO under influence of DMSO, topotecan, OL9-119 and its combination (topotecan+OL9-119). Wild type control samples fastq files were uploaded under GSE218871.

TDP1是一种在人类体内由TDP1基因编码的酶[5][6][7]。TDP1是参与修复停滞的拓扑异构酶I-DNA复合物的蛋白质。本研究评估了HEK293A细胞中Tdp1敲除对基因表达的影响。我们采用CRISPR/Cas9方法构建了Tdp1敲除的HEK293A细胞系，向导RNA（gRNA）靶向Tdp1基因的组成型蛋白编码外显子区域进行设计。随后，我们对野生型HEK293A细胞与Tdp1-KO细胞分别在二甲基亚砜（DMSO）、拓扑替康（topotecan）、OL9-119以及二者联合处理（拓扑替康+OL9-119）条件下的RNA测序（RNA-seq）数据开展了比较基因表达谱分析。野生型对照样本的fastq文件已上传至GSE218871。