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Genome-wide DNA methylation analysis using MethylCap-seq in canine diffuse large B-cell (cDLBCL) cell lines

ABSTRACT: Genome-wide DNA methylation analysis using MethylCap-seq in canine diffuse large B-cell (cDLBCL) cell lines

PROVIDER: PRJNA630576 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11697805_1.fastq.gz	Fastqsanger.gz
	SRR11697805_2.fastq.gz	Fastqsanger.gz
	SRR11697806_1.fastq.gz	Fastqsanger.gz
	SRR11697806_2.fastq.gz	Fastqsanger.gz
	SRR11697807.fastq.gz	Fastqsanger.gz

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Genome-wide DNA methylation analysis using MethylCap-seq in canine diffuse large B-cell (cDLBCL) cell lines

Project description:MethylCap-seq was performed to characterize the genome-wide DNA methylation in CLBL-1 8.0, a doxorubicin-resistant cDLBCL cell line, and CLBL-1 as control, and aimed to investigate underlying mechanisms of doxorubicin resistance in cDLBCL. Strong difference in methylation pattern of both promoter and gene-body regions was detected between CLBL-1 8.0 and CLBL-1. Methylated peaks with fold-change greater than 4 and a P value of less than 0.01 were defined as differentially methylated regions (DMRs); there were a total of 20289 hypermethylated and 38362 hypomethylated DMRs detected. Among these, 1339 hypermethylated and 4861 hypomethylated DMRs were in promoter regions, while 12855 hypermethylated and 18904 hypomethylated DMRs were in gene-body regions. There were 6.6% hypermethylated DMRs located on the promoter regions. A high percentage (63.4%) of hypermethylated DMRs were distributed within the gene body, and 7.8%, 5.1% and 23.8% hypermethylated DMRs were found to be clustered in upstream, downstream, and intergenic regions, respectively.

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Project description:To analyze the biological relevance of methylation changes, gene expression from both CLBL-1 and CLBL-1 8.0, a doxorubicin-resistanct cDLBCL cell line, were examined. In total, we obtained 24.8 M and 23.7 M sequence reads for CLBL-1 and CLBL-1 8.0, respectively. After filtering out low-quality bases and reads from the datasets prior to read mapping, 19.8 M reads for CLBL-1 and 19.1 M reads for CLBL-1 8.0 were mapped to canine genome. The criteria that transcripts per million (TPM) >5 in one of sample and the log2 fold-change ≥ 0.67 or ≤ -0.67 were applied to identified differentially expressed genes. Upregulated and downregulated genes were 1127 and 602, respectively.

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