Supporting data and materials for "Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat".
Dataset type: Software, Epigenomic
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. https://doi.org/10.5524/100167
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., Mikeska, T., van Denderen, B. J. W., Thompson, E. W., Eggers, S., Doyle, S. R., & Dobrovic, A. (2015). Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat. GigaScience, 4(1). https://doi.org/10.1186/s13742-015-0098-x
Accessions (data included in GigaDB):
Click on a table column to sort the results.
Table SettingsSample ID | Common Name | Scientific Name | Sample Attributes | Taxonomic ID | Genbank Name |
---|---|---|---|---|---|
12A-CD19 | Human | Homo sapiens | Description:Normal Fluorescent Activated Cell Sorted (FACS) CD19 positive bone marrow cells from individual 12A Alternative accession-GEO:GSM1657259 |
9606 | human |
12A-CD33 | Human | Homo sapiens | Alternative accession-GEO:GSM1657260 Description:Normal Fluorescent Activated Cell Sorted (FACS) CD33 positive bone marrow cells from individual 12A |
9606 | human |
12A-CD34 | Human | Homo sapiens | Description:Normal Fluorescent Activated Cell Sorted (FACS) CD34 positive bone marrow cells from individual 12A Alternative accession-GEO:GSM1657261 |
9606 | human |
12A-CD45 | Human | Homo sapiens | Alternative accession-GEO:GSM1657262 Description:Normal Fluorescent Activated Cell Sorted (FACS) CD45 positive bone marrow cells from individual 12A |
9606 | human |
293 | Human | Homo sapiens | Alternative accession-GEO:GSM1657263 Description:HEK-293 embryonic kidney cell line. ATCC CRL1573 |
9606 | human |
40424 | Human | Homo sapiens | Description:Normal fibroblast cell line Alternative accession-GEO:GSM1657264 |
9606 | human |
6-MDA453 | Human | Homo sapiens | Description:MDA-MB-453 metastatic breast cancer cell line. ATCC HTB-131 Alternative accession-GEO:GSM1657265 |
9606 | human |
6C-CD19 | Human | Homo sapiens | Alternative accession-GEO:GSM1657266 Description:Normal Fluorescent Activated Cell Sorted (FACS) CD19 positive bone marrow cells from individual 6C |
9606 | human |
6C-CD33 | Human | Homo sapiens | Alternative accession-GEO:GSM1657267 Description:Normal Fluorescent Activated Cell Sorted (FACS) CD33 positive bone marrow cells from individual 6C |
9606 | human |
6C-CD34 | Human | Homo sapiens | Description:Normal Fluorescent Activated Cell Sorted (FACS) CD34 positive bone marrow cells from individual 6C Alternative accession-GEO:GSM1657268 |
9606 | human |
Click on a table column to sort the results.
Table SettingsFile Name | Description | Sample ID | Data Type | File Format | Size | Release Date | File Attributes | Download |
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Readme | TEXT | 462 B | 2015-11-11 | MD5 checksum: 1e3ebbc5ca425daf7d0b7e0617c3cdf7 |
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Sorted BAM file | Methylome data | BAM | 4.27 MB | 2015-11-11 | MD5 checksum: 46b76c6e44b870cce95ce1d6580bdca6 |
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Raw BAM file after Bismark aligment | Methylome data | BAM | 5.54 MB | 2015-11-11 | MD5 checksum: 3c8dfe31bcf417ebde563d907fab4eee |
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Sorted BAM file | Methylome data | BAM | 6.07 MB | 2015-11-11 | MD5 checksum: 53f468ceefc1030177a903447a2f1765 |
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Raw BAM file after Bismark aligment | Methylome data | BAM | 8.20 MB | 2015-11-11 | MD5 checksum: d8ff52c217b009a6dca5504d58567b51 |
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Sorted BAM file | Methylome data | BAM | 7.45 MB | 2015-11-11 | MD5 checksum: 86da6fb984397e3e91f03ccbe5d35055 |
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Raw BAM file after Bismark aligment | Methylome data | BAM | 10.48 MB | 2015-11-11 | MD5 checksum: bc5d96fc85d3399e31b48ffda7110103 |
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Sorted BAM file | Methylome data | BAM | 11.48 MB | 2015-11-11 | MD5 checksum: 980474518ac40af6f324146764cfd21c |
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Raw BAM file after Bismark aligment | Methylome data | BAM | 15.26 MB | 2015-11-11 | MD5 checksum: f449034c60611a8329d412dd62ad297f |
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Sorted BAM file | Methylome data | BAM | 2.62 MB | 2015-11-11 | MD5 checksum: 315c0c852acf0f741488086f27a1cc76 |
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 |
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November 24, 2015 | Dataset publish |
November 27, 2015 | Manuscript Link added : 10.1186/s13742-015-0098-x |
May 1, 2020 | File readme.txt updated |