Project description:To explore the roles of cell-type specific methylation QTL (meQTL) for melanoma GWAS annotation, we generated DNA methylation data from the same sample set as our previouse eQTL study including 106 primary melanocyte cultures. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs in 106 primary melanocyte cultures. To be able to identify the DNA methylation probes whose methylation levels are correlated with germline genetic variants including the ones associated with melanoma, meQTL analysis was performed in these 106 primary melanocyte cultures using the same method as we did for eQTL study.
Project description:Melanoblastoma-bearing Libechov minipigs (MeLiM) provide an animal model for the study of spontaneous cutaneous melanoma. We compared the serial analysis of gene expression (SAGE) profile between normal skin melanocytes and melanoma cells from a pulmonary metastasis of MeLiM. Keywords: disease state study To minimise the contribution of cells other than melanocytes, we constructed SAGE libraries from a primary culture of melanoma cells derived from a pulmonary melanoma metastasis of a young MeLiM and from a pigmented melanocyte cell line, PigMel, derived from the skin of a healthy Meishan pig.
Project description:Capture-HiC was conducted to map chromatin interactions at all melanoma GWAS identified risk-associated regions across five individual primary human melanocyte cultures. Capture-HiC baits were designed by Arima Genomics (San Diego, CA, 2x tiling, least stringent masking, XTHSBoosting) to obtain an Agilent Sure Select library (Santa Clara, CA) targeting all restriction fragments (recognition sequences: ^GATC, ^GANTC) covering entire regions of association for the 68 independent genome-wide significant signals. Fifteen Capture-HiC libraries were generated from five human primary melanocyte cultures (C56, C140, C205, C24, and C27), with three technical replicates for each culture, except C56 third technical replicate, where the same library was also sequenced in a different batch labeled as rep4. The barcoded Capture-HiC libraries were pooled and sequenced using an Illumina Novaseq. This included one run on an SP flow cell and a second run on an S1 flow cell, resulting in approximately 5.7 billion paired-end reads with a read length of 150 bp. This sequencing yielded a median coverage of about 350 million read pairs per technical replicate and approximately 1.1 billion read pairs per culture.