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Circadian 30-h time-course RNA-seq study of SW480 and SW620 cells

ABSTRACT: Circadian 30-h time-course RNA-seq study of SW480 and SW620 cells

PROVIDER: PRJEB31695 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR3219930_1.fastq.gz	Fastqsanger.gz
	ERR3219930_2.fastq.gz	Fastqsanger.gz
	ERR3219940_1.fastq.gz	Fastqsanger.gz
	ERR3219940_2.fastq.gz	Fastqsanger.gz
	ERR3219950_1.fastq.gz	Fastqsanger.gz

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Circadian 30-h time-course RNA-seq study of SW480 and SW620 cells

Project description:A 30-h time-course RNA-seq study was performed to analyse the different circadian phenotypes of SW480 and SW620 cells, a cell line from a primary tumour and a metastatic cell line from the same patient. Samples were taken every 3 h for a period of 30 h resulting in 11 time-points for each cell line.

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Project description:Two isogenic human colorectal cancer cell lines (primary SW480 cell line and its lymph node metastatic variant SW620 cell line),as an in vitro metastatic model. We have demonstrated that SW620 cell line possesses high metastasis potential and SW480 cell linepossesses low metastatic potential. We want to compare the whole cell microRNAs profiles of two isogenic colorectal cancer cell lines (SW480 and SW620 cell line), to gain an insight into the molecular events of colon cancer metastasis.

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Wnt signaling inhibition in human colon cancer cell lines (SW480 and SW620) drives changes in gene programs for cell adhesion, mobility, and cell junction

Project description:Overactive Wnt signaling has been found to be a significant driver in colon cancer carcinogenesis targeting many cellular processes such as cel proliferation, migration, and metabolism. The purpose of this study was to use high throughput transcriptional profiling (RNA-seq) to identify Wnt signaling gene targets in human colon cancer cells. Transcriptional profiles of human colon cancer cell lines (SW480 and SW620) with overactive Wnt signaling were compared to their matching Wnt low genetically modified stable cell (SW480-dnLEF1 and SW620-dnLEF1) through high throughput RNA-seq with four biological replicates. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat2 followed by HTseq and DESEQ2. Using an optimized data analysis workflow, we mapped about 30-40 million sequence reads per sample to the human genome (build hg38). RNAseq analysis of dnLEF1 expression in SW480 and SW620 cells cultured in vitro showed changes in gene programs for cell adhesion, mobility, cell junction, and extracellular matrix.

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