Resources for the MeDUSA (Methylated DNA Utility for Sequence Analysis) MeDIP-seq computational analysis pipeline for the identification of differentially methylated regions, and associated methylome data from 18 wild-type and mutant mouse ES, NP and MEF cells.
Dataset type: Epigenomic
Data released on June 27, 2012
Wilson GA; Dharmi P; Saito Y; Cortazar D; Kunz C; Schär P; Beck S (2012): Resources for the MeDUSA (Methylated DNA Utility for Sequence Analysis) MeDIP-seq computational analysis pipeline for the identification of differentially methylated regions, and associated methylome data from 18 wild-type and mutant mouse ES, NP and MEF cells. GigaScience. https://doi.org/10.5524/100035
Here we present 18 genome-wide DNA methylation profiles of wild type and Thymine DNA glycosylase (Tdg) knockout cells, which serve as an excellent murine methylome resource. The 18 samples represent 6 biological cohorts: 6 samples were derived from mouse embryonic stem cells (3 Tdg+/-, 3 Tdg-/-), 6 samples were from mouse neural precursor cells (3 Tdg+/-, 3 Tdg-/-) and 6 samples were obtained from mouse embryonic fibroblasts (3 Tdg+/+, 3 Tdg-/-). Next generation sequencing was performed on the libraries using an Illumina GAIIx for each sample. Paired end alignment against the mouse genome (Build NCBIM37) was performed using BWA (v0.5.8), and filtering to remove those reads failing to map was performed using SAMtools (v0.1.9) and a custom perl script. The Bioconductor (v2.7) package MeDIPs (v1.0.0) was used to normalize for size of the sequence library, done by calculating reads per million in tiled windows across the genome. Fragment length normalization was performed using a custom perl script. Wig tracks representing library size normalized alignment were generated using a combination of MEDIPS and custom R scripts. In addition to the total alignment wig track, strand specific wig tracks were also generated, enabling the user to infer whether the MeDIP signal is derived by methylation on the forward and/or reverse strand. The MeDIP-seq data were processed using the analysis pipeline MeDUSA (Methylated DNA Utility for Sequence Analysis). MeDUSA brings together numerous software packages to perform a full analysis of MeDIP-seq data, including sequence alignment, quality control, and determination and annotation of differentially methylated regions.
Additional details
Read the peer-reviewed publication(s):
- Wilson, G. A., Dhami, P., Feber, A., Cortázar, D., Suzuki, Y., Schulz, R., Schär, P., & Beck, S. (2012). Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers. GigaScience, 1(1). https://doi.org/10.1186/2047-217x-1-3 (PubMed:23587164)
Additional information:
http://projects.ensembl.org/heroic/
http://www2.cancer.ucl.ac.uk/medicalgenomics/tdg_web/trackList.php
http://www2.cancer.ucl.ac.uk/medicalgenomics/medusa/
Accessions (data included in GigaDB):
GEO: GSE27468
SRA: SRP005934
BioProject: PRJNA138437
Projects:
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Table SettingsSample ID | Common Name | Scientific Name | Sample Attributes | Taxonomic ID | Genbank Name |
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SRS173539 | Mouse | Mus musculus | Antibody-catalog number:BI-MECY-0100 Description:source: Mouse embryonic stem cells Genetic background:129 C57BL/6 mixed ... |
10090 | house mouse |
SRS173540 | Mouse | Mus musculus | Antibody-lot number:Lot:070809 Antibody-catalog number:BI-MECY-0100 Antibody-manufacturer:Eurogentec ... |
10090 | house mouse |
SRS173541 | Mouse | Mus musculus | Antibody-lot number:Lot:070809 Antibody-manufacturer:Eurogentec Cell type:embryonic stem cells ... |
10090 | house mouse |
SRS173542 | Mouse | Mus musculus | Antibody-catalog number:BI-MECY-0100 Antibody-lot number:Lot:070809 Cell type:embryonic stem cells ... |
10090 | house mouse |
SRS173543 | Mouse | Mus musculus | Antibody-lot number:Lot:070809 Antibody-catalog number:BI-MECY-0100 Antibody-manufacturer:Eurogentec ... |
10090 | house mouse |
SRS173544 | Mouse | Mus musculus | Antibody-catalog number:BI-MECY-0100 Antibody-lot number:Lot:070809 Antibody-manufacturer:Eurogentec ... |
10090 | house mouse |
SRS173545 | Mouse | Mus musculus | Antibody-catalog number:BI-MECY-0100 Antibody-lot number:Lot:070809 Antibody-manufacturer:Eurogentec ... |
10090 | house mouse |
SRS173546 | Mouse | Mus musculus | Antibody-catalog number:BI-MECY-0100 Antibody-lot number:Lot:070809 Antibody-manufacturer:Eurogentec ... |
10090 | house mouse |
SRS173547 | Mouse | Mus musculus | Antibody-lot number:Lot:070809 Antibody-catalog number:BI-MECY-0100 Antibody-manufacturer:Eurogentec ... |
10090 | house mouse |
SRS173548 | Mouse | Mus musculus | Antibody-catalog number:BI-MECY-0100 Antibody-lot number:Lot:070809 Antibody-manufacturer:Eurogentec ... |
10090 | house mouse |
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Table SettingsFile Name | Description | Sample ID | Data Type | File Format | Size | Release Date | File Attributes | Download |
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Readme | TEXT | 1.19 kB | 2012-06-27 | MD5 checksum: 9dd4855052ea0306d898fe571c91c3b0 |
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ISA-Tab investigation | ISA-Tab | TEXT | 7.43 kB | 2012-06-27 | MD5 checksum: 05af55de3fc455ad9681d638fd430a54 |
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ISA-Tab sample | ISA-Tab | TEXT | 5.84 kB | 2012-06-27 | MD5 checksum: eff25a2890ef825220a29f1daebc7f41 |
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ISA-Tab assay | ISA-Tab | TEXT | 509.82 kB | 2012-06-27 | MD5 checksum: 790b1ed9b9b236bc234db592d78cf7b4 |
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MeDUSA version 1.0.0 | Software | TAR | 561.45 MB | 2012-06-27 | MD5 checksum: 39fe53acd4ca2bf894fbe53fdacd345f |
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Alignments | BAM | 3.61 GB | 2012-06-27 | MD5 checksum: 35d89e9b8f0b9cdbdd65ffdb8c2ec584 |
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Alignments | BAM | 3.45 GB | 2012-06-27 | MD5 checksum: 76c277a8f336c88c107afd57f58eced0 |
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Alignments | BAM | 3.10 GB | 2012-06-27 | MD5 checksum: f38c1da08df11b4474d78f91ccb92a24 |
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Alignments | BAM | 3.88 GB | 2012-06-27 | MD5 checksum: f71d65ca2856e04c68ac40bc8427f182 |
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Alignments | BAM | 3.78 GB | 2012-06-27 | MD5 checksum: c1943240ac40c8cac5436b0c8e14bf20 |
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