Supporting data and materials for "Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat".

Dataset type: Epigenomic, Software
Data released on November 24, 2015

Wong NC; Pope BJ; Candiloro I; Korbie D; Trau M; Wong SQ; Mikeska T; van Denderen BJ; Thompson EW; Eggers S; Doyle S; Dobrovic A (2015): Supporting data and materials for "Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat". GigaScience Database. http://dx.doi.org/10.5524/100167

DOI10.5524/100167

DNA methylation is a complex epigenetic marker that can be analysed using a wide variety of methods. Interpretation and visualisation of DNA methylation data can mask complexity in terms of methylation status at each CpG site, cellular heterogeneity of samples and allelic DNA methylation patterns within a given DNA strand. Bisulfite sequencing is considered the gold standard, however visualisation of massively parallel sequencing results remains a significant challenge.
We created a program called Methpat that facilitates visualisation and interpretation of bisulfite sequencing data generated by massively parallel sequencing. To demonstrate this, we performed multiplex PCR that targeted 48 regions of interest across 86 human samples. The regions selected included known gene promoters associated with cancer, repetitive elements, known imprinted regions and mitochondrial genomic sequences. We interrogated a range of samples including human cell lines, primary tumours and primary tissue samples. Methpat generates two forms of output: a tab delimited text file for each sample that summarises DNA methylation patterns and their read counts for each amplicon and a HTML file that summarises this data visually. Methpat can be used with publicly available whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) datasets with sufficient read depths.
Using Methpat, complex DNA methylation data derived from massively parallel sequencing can be summarised and visualised for biological interpretation. By accounting for allelic DNA methylation states and their abundance in a sample, Methpat can unmask the complexity of DNA methylation and reveal further biological insight in existing datasets.

Additional details

Read the peer-reviewed publication(s):

Wong, N. C., Pope, B. J., Candiloro, I., Korbie, D., Trau, M., Wong, S. Q., … Dobrovic, A. (2015). Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat. GigaScience, 4(1). doi:10.1186/s13742-015-0098-x

Accessions (data generated as part of this study):

GEO: GSE67856
GEO: GSE71804





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
12A-CD199606HumanhumanHomo sapiens Description:Normal Fluorescent Activated Cell Sorted (FACS) CD19 positive bone marrow cells from individual 12A
Alternative accession-GEO:GSM1657259
12A-CD339606HumanhumanHomo sapiens Description:Normal Fluorescent Activated Cell Sorted (FACS) CD33 positive bone marrow cells from individual 12A
Alternative accession-GEO:GSM1657260
12A-CD349606HumanhumanHomo sapiens Description:Normal Fluorescent Activated Cell Sorted (FACS) CD34 positive bone marrow cells from individual 12A
Alternative accession-GEO:GSM1657261
12A-CD459606HumanhumanHomo sapiens Description:Normal Fluorescent Activated Cell Sorted (FACS) CD45 positive bone marrow cells from individual 12A
Alternative accession-GEO:GSM1657262
2939606HumanhumanHomo sapiens Description:HEK-293 embryonic kidney cell line. ATCC CRL1573
Alternative accession-GEO:GSM1657263
404249606HumanhumanHomo sapiens Description:Normal fibroblast cell line
Alternative accession-GEO:GSM1657264
468-C1-3-9_S899606HumanhumanHomo sapiens Description:MDA-468 cell line, control 1
Alternative accession-GEO:GSM1846123
468-C2-3-9_S909606HumanhumanHomo sapiens Description:MDA-468 cell line, control 2
Alternative accession-GEO:GSM1846122
468-S1-3-9_S919606HumanhumanHomo sapiens Description:MDA-468 cell line +EGF 1
Alternative accession-GEO:GSM1846124
468-S2-3-9_S929606HumanhumanHomo sapiens Description:MDA-468 cell line +EGF 2
Alternative accession-GEO:GSM1846125
Displaying 1-10 of 86 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
12A-CD19Methylome dataBAM5.28 MB2015-11-11
12A-CD19Methylome dataTEXT1.45 KB2015-11-11
12A-CD19Methylome dataBAM4.07 MB2015-11-11
12A-CD33Methylome dataBAM14.55 MB2015-11-11
12A-CD33Methylome dataTEXT1.45 KB2015-11-11
12A-CD33Methylome dataBAM10.95 MB2015-11-11
12A-CD34Methylome dataBAM7.82 MB2015-11-11
12A-CD34Methylome dataTEXT1.45 KB2015-11-11
12A-CD34Methylome dataBAM5.79 MB2015-11-11
12A-CD45Methylome dataBAM9.99 MB2015-11-11
Displaying 1-10 of 782 File(s).
Funding body Awardee Award ID Comments
National Breast Cancer Foundation CG-08-07
National Breast Cancer Foundation CG-10-04
National Breast Cancer Foundation CG-12-07
National Health and Medical Research Council APP1027527
Victorian Cancer Agency
Victor Smorgon Charitable Fund
Date Action
November 24, 2015 Dataset publish
November 27, 2015 Manuscript Link added : 10.1186/s13742-015-0098-x