GSM4815813: 349C; Homo sapiens; Bisulfite-Seq
For each patient, five 1 mm tumour tissue cores from within the histologically verified tumour region (or tumour adjacent region) were taken for genomic DNA extraction. DNA was extracted using the AllPrep FFPE DNA/RNA Kit (Qiagen, Cat. No. 80234), quantified with the Qubit dsDNA HS Assay Kit (Life Technologies, USA), and stored at -80 °C until use. For library preparation of patient specimens extracted DNA were bisulphite treated using the EZ DNA Methylation-Lightning Kit (Zymo Research, USA, Cat. No. D5030 & D5033) according to the manufacturer's instructions. DNA methylation profiling was performed using WGBS). WGBS libraries were prepared using the EpiGnome Methyl-Seq kit (Epicentre, EGMK81312), according to the manufacturer's protocol. Library quality was assessed with the Agilent 2100 Bioanalyzer using the High-sensitivity DNA kit (Agilent, CA, USA). DNA was quantified using the KAPA Library Quantification kit by quantitative PCR (KAPA 6 Biosystems). Libraries from patient specimens were analysed with 70 bp paired end sequencing on the Illumina HiSeq 2500 platform using TruSeq® Rapid SBS Kit – HS (50 cycle) and TruSeq® Rapid PE Cluster Kit – HS. 6 samples were multiplexed across 2 lanes. Sequencing was performed multiple times to gain sufficient coverage.
GEO Accession
GSM4815813