Regulatin of KDM5C stability and enhancer reprogramming in breast cancer [RNA-seq]

Purpose: Purpose:Exploring genes regulated by trim11 and kdm5c in breast cancer Methods: TRIM11 knock down and KDM5C knock down MDA-MB-231 cell lines were constructed and Trim11 knock down MMTV mice were generated. The RNA-seq libraries of cell lines and mice mammary tumors were sequenced by Illumina Nova-seq platform with pair-end reads of 150 bp. Results: Quality control of mRNA-seq data was performed using Fatsqc and low-quality bases were trimmed. The adaptor sequence was removed using Cutadapt (version 1.16) to clean RNA-seq raw data. All RNA-seq data were mapped to the human reference genome (hg19) or mouse reference genome (mm10) by HISAT2 (version 2.1.0). The gene expression level was calculated by Cufflinks with default parameters. Differential expressed genes (DEGs) were identified by 1.5-fold change and p-value < 0.05. Gene ontology analysis and KEGG pathways analysis was performed using DAVID (https://david.ncifcrf.gov). Conclusions: Our study represents biological process and KEGG pathway enrichment analyses of TRIM11 and KDM5C down-regulated genes or up-regulated genes mRNA profiles of control, TRIM11 knockdown, KDM5C knockdown and double knockdown MDA-MB-231 breast cancer cells. mRNA profiles of wide type(WT) and Trim11+/- MMTV mice breast tumors

研究目的：探究乳腺癌中受TRIM11与KDM5C调控的基因。
实验方法：构建TRIM11敲低与KDM5C敲低的MDA-MB-231细胞系，并生成Trim11敲低的MMTV小鼠模型。采用Illumina Nova-seq测序平台，以150 bp双端读长对细胞系及小鼠乳腺肿瘤的RNA-seq文库进行测序。
实验结果：对mRNA-seq数据的质量控制采用Fastqc完成，并对低质量碱基进行修剪；使用Cutadapt（版本1.16）移除接头序列以清理RNA-seq原始数据。所有RNA-seq数据通过HISAT2（版本2.1.0）比对至人类参考基因组（hg19）或小鼠参考基因组（mm10）。基因表达水平采用Cufflinks以默认参数计算。通过1.5倍表达变化差异及p值<0.05筛选差异表达基因（Differential Expressed Genes, DEGs）。使用DAVID（https://david.ncifcrf.gov）完成基因本体（Gene Ontology, GO）富集分析与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）通路分析。
研究结论：本研究涵盖了对照组、TRIM11敲低组、KDM5C敲低组及双敲低组MDA-MB-231乳腺癌细胞中，受TRIM11与KDM5C调控的上调、下调基因的mRNA表达谱的生物学过程及KEGG通路富集分析；同时涵盖野生型（Wild Type, WT）及Trim11+/- MMTV小鼠乳腺肿瘤的mRNA表达谱。