Project description:Single cell technologies have paved the way for the characterization of colorectal cancer.We performed scRNA-seq on human colorectal tumors and their matched adjacent-normal tissues and liver metastasis tissue. The heterogneity of the tumor immune microenvironment were analyzed.
Project description:To identify the gene expression of early-onset colorectal cancer, we sampled early-onset colorectal cancer patients (age < 50) and late-onset colorectal cancer paitients (age > 70) We then performed gene expression profiling analysis using data obtained from RNA-seq of early-onset colorectal cancer tissues and late-onset colorectal cancer tissues.
Project description:To identifythe the functional roles of circRNAs in human colorectal cancer, we analysed the differenial expression of circRNAs in 5 colorectal cancer tissues and the corresponding non-cancerous tissues. We used microarrays to detail the global programme of circRNA expression in human colorectal cancer tissues and correponding non-cancerous tissues.
Project description:To identify novel hypermethylated genes in colorectal cancer (CRC) and to test their potential application in CRC early diagnosis, we performed a genome-wide screening of 57,723 CpG dinucleotides covering 4,010 genes in paired DNA samples extracted from 3 fresh frozen CRC tissues and their matching non-tumor adjacent tissues from a cohort of 3 CRC patients undergoing curative surgery using MIRA-based microarray. We also validated candidate hypermethylated genes screened by MIRA-based microarray in independent CRC samples using combined bisulfite restriction analysis. A total of 297 CpG dinucleotides in CRC covering 211 genes were found to be hypermethylated in CRC tissues. From these 211 candidate methylated genes, seven novel methylated genes were picked up for validation and three genes were confirmed to be methylated in cancer samples but not in non-cancer samples.We also compared the methylation levels of these three novel hypermethylated genes with those of Vimentin and SEPT9, well-known hypermethylated genes in CRC, and found that methylated PHOX2B, FGF12 and GAD2 were better than methylated Vimentin and SEPT9 in differentiating CRC cancer tissue from normal tissue. Significant enrichment analysis of GO terms of the hypermethylated genes showed that a high proportion of hypermethylated genes in tumor tissues are involved in regulation of transcription. Paired experiments, colorectal cancer tissue vs. adjacent non-cancer tissue. Biological replicates: 3 cancer replicates, 3 paired non-cancer replicates.
Project description:To identify ythe the functional roles and the pathophysiological contributions of coding genes and noncoding RNAs in human colorectal carcinogenesis, we analysed the differenial expression of genes and noncoding RNAs in colorectal cancer tissues and the corresponding non-cancerous tissues.
Project description:Total RNA from 6 pairs colorectal cancer tissues and its matched adjacent non-cancerous tissues was extracted and sequenced by high throughput sequencing. Then, differentially expressed circRNAs, long noncoding RNAs, and mRNAs were showed in colorectal cancer.