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Whole DNA methylome profiling in lung cancer cells before and after epithelial-to-mesenchymal transition

Fatao Liu1, Yi Zhou1, Daizhan Zhou2, Mengyuan Kan1, Xiaomin Niu3, Zhou Zhang2, Di Zhang2, Liming Tao1, Lin He124, Lixing Zhan1* and Yun Liu45*

Author Affiliations

1 Institute for Nutritional Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 320 Taiyuan RD, Shanghai 200031, PR China

2 Bio-X Institute, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, PR China

3 Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, PR China

4 Institute of Biomedical Sciences, Fudan University, Shanghai 200032, PR China

5 Key Laboratory of Molecular Medicine, The Ministry of Education, Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, 138 YiXueYuan RD, Shanghai 200032, PR China

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Diagnostic Pathology 2014, 9:66  doi:10.1186/1746-1596-9-66

Published: 20 March 2014

Additional files

Additional file 1: Figure S1:

The effect of sequencing depth on the accuracy of methylation level estimation. For each level of sequencing depth, the methylation of all the CCGG sites involved was showed (S0h on x-axis and S24h on y-axis). As the sequencing depth increases the Pair-wise correlation coefficient increases, which indicates that the sequencing data is more believable. Figure S2. The overall methylation of each chromosome of primary A549 cells. The mitochondrial genome and Y chromosome show significantly high methylation level. The average methylation level of other chromosomes is approximately 20%. Figure S3. The methylation level of CCGG sites with 30+ reads in S4h, S12h, S24h and S4d compared with S0h. The Pair-wise correlation coefficients are showed and a similarity between cells before and after EMT is observed. Table S1. List of antibodies used for western blot. Table S2. List of primers used for qRT-PCR. Table S3. List of Index used in second-generation sequencing. Table S4. Summary of second-generation sequencing data in MSCC-seq. Table S5. The top 20 genes with the highest and lowest average methylation level around TSS region.

Format: DOCX Size: 2.2MB Download file

Open Data

Additional file 2: Table S6:

The methylation level and annotation information of CCGGs quantified both in S0h, S4h, S12h, S24h and S4d.

Format: XLSX Size: 19.3MB Download file

Open Data