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Open Access Highly Accessed Research article

Genome-wide promoter methylation profile of human testis and epididymis: identified from cell-free seminal DNA

Chunlin Wu1, Xiaofang Ding2, Honggang Li13*, Changhong Zhu13 and Chengliang Xiong13

Author Affiliations

1 Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China

2 Centre of Reproductive Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China

3 Wuhan Tongji Reproductive Medicine Hospital, Wuhan, 430013, China

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BMC Genomics 2013, 14:288  doi:10.1186/1471-2164-14-288

Published: 28 April 2013

Additional files

Additional file 1:

The lists of testis and epididymis-specific hypo- and hypermethylated genes.

Format: XLSX Size: 110KB Download file

Open Data

Additional file 2:

The Ct value of 10 validated genes in IP and Input DNA identified by MeDIP-real time quantitative PCR and the relative quantity of IP/Input in the cfsDNA of Nor and PV.

Format: XLSX Size: 12KB Download file

Open Data

Additional file 3:

The methylation status of 9 promoters analyzed by MethyLight. Box plots illustrating the methylation level of amplifiable promoter fragments measured by MethyLight between the bisulfite-converted cfsDNA of 4 Nor and 4 PV. Methylation targets are promoter sequences specific to the 3 testis and epididymis-specific hypermethylated genes (CHRFAM7A, USP28 and NCK2) and 6 testis and epididymis-specific hypomethylated genes (ERRFI1, FBRS, GLTPD1, HSF1, VPS16 and ZNF623) identified by promoter methylation microarray. The boxes represent the quartiles and whiskers mark the range of the data, the horizontal line in the boxes denotes the median.

Format: PDF Size: 880KB Download file

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Open Data

Additional file 4:

The Ct value of 9 validated genes identified by MethyLight analysis and the relative methylation level of target genes in the cfsDNA of Nor and PV.

Format: XLSX Size: 21KB Download file

Open Data

Additional file 5:

GO enrichment analysis of the testis and epididymis-specific hypomethylated genes. Each bar represents the enrichment score (ES) of significant GO terms. The ES of each GO terms is larger than 1.0. The number in brackets denotes the quantity of genes involved in each GO term.

Format: PDF Size: 911KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6:

GO enrichment analysis of the testis and epididymis-specific hypermethylated genes. Each bar represents the enrichment score (ES) of significant GO terms. The ES of each GO terms is larger than 1.0. The number in brackets denotes the quantity of genes involved in each GO term.

Format: PDF Size: 845KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 7:

Primers used for MeDIP-real time quantitative PCR.

Format: XLSX Size: 11KB Download file

Open Data

Additional file 8:

Primers and probes used for MethyLight analysis.

Format: XLSX Size: 12KB Download file

Open Data