Genome-wide DNA Methylation Landscape of NSCLC
Description
Genome-wide DNA methylation profiling using Reduced Representation Bisulfite Sequencing (RRBS) on 260 methylomes from paired tumour and adjacent non-cancerous lung tissues of 130 NSCLC patients - 54 adenocarcinoma (AC), 72 squamous cell carcinoma (SCC). Snap-frozen tumour and matched non-malignant tissues (260 samples) were processed for DNA extraction (DNeasy Blood & Tissue Kit, Qiagen) and quality control. Genomic DNA (1.2 µg) was used for RRBS (Reduced Representation Bisulfite Sequencing) library preparation (NEXTflex Bisulfite-Seq Kit, BIOO Scientific) and sequenced on Illumina HiSeq 4000 (Illumina, San Diego, USA) in paired-end (PE) mode (2 × 76 cycles). FASTQ files were generated with bcl2fastq (Illumina, San Diego, USA), quality-checked with FastQC (Babraham Institute) and MultiQC, and cleaned with BBduk (DOE JGI, USA) with RRBS-specific parameters. Reads were aligned to GRCh37 (Ensembl 75) using Bismark (Babraham Institute)15 in PE mode, and CpG methylation calls extracted in no-overlap mode after M-bias evaluation. Dataset represent DNA methylation calls in CpG regions with coverage >=10x in bedgraph file with combined samles from tumor (T) and non-cancerous (N) samples. There are three datasets: 1) all NSCLC patients, 2) only adenocarcinoma (AC) patients, 3) only squamous cell carcinoma (SCC) patients.
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Institutions
- Uniwersytet Medyczny w BialymstokuBialystok