Help Login Create account

Data released on June 27, 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.

Beck, S; Cortazar, D; Dharmi, P; Kunz, C; Saito, Y; Schär, P; Wilson, G, A (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. http://dx.doi.org/10.5524/100035 RIS BibTeX Text

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.

Contact Submitter

Related manuscripts:

doi: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:


Epigenomic

http://gigadb.org/images/data/cropped/100035_mouse_methylome.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SRS17353910090Mousehouse mouseMus musculus Antibody-catalog number:BI-MECY-0100
Antibody-lot number:Lot:070809
Antibody-manufacturer:Eurogentec
...
+
SRS17354010090Mousehouse mouseMus musculus Antibody-catalog number:BI-MECY-0100
Antibody-lot number:Lot:070809
Antibody-manufacturer:Eurogentec
...
+
SRS17354110090Mousehouse mouseMus musculus Antibody-catalog number:BI-MECY-0100
Antibody-lot number:Lot:070809
Antibody-manufacturer:Eurogentec
...
+
SRS17354210090Mousehouse mouseMus musculus Antibody-catalog number:BI-MECY-0100
Antibody-lot number:Lot:070809
Antibody-manufacturer:Eurogentec
...
+
SRS17354310090Mousehouse mouseMus musculus Antibody-catalog number:BI-MECY-0100
Antibody-lot number:Lot:070809
Antibody-manufacturer:Eurogentec
...
+
SRS17354410090Mousehouse mouseMus musculus Antibody-catalog number:BI-MECY-0100
Antibody-lot number:Lot:070809
Antibody-manufacturer:Eurogentec
...
+
SRS17354510090Mousehouse mouseMus musculus Antibody-catalog number:BI-MECY-0100
Antibody-lot number:Lot:070809
Antibody-manufacturer:Eurogentec
...
+
SRS17354610090Mousehouse mouseMus musculus Antibody-catalog number:BI-MECY-0100
Antibody-lot number:Lot:070809
Antibody-manufacturer:Eurogentec
...
+
SRS17354710090Mousehouse mouseMus musculus Antibody-catalog number:BI-MECY-0100
Antibody-lot number:Lot:070809
Antibody-manufacturer:Eurogentec
...
+
SRS17354810090Mousehouse mouseMus musculus Antibody-catalog number:BI-MECY-0100
Antibody-lot number:Lot:070809
Antibody-manufacturer:Eurogentec
...
+
Displaying 1-10 of 18 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
ISA-TabTEXT497.87 KB2012-06-27
SAMPLE:SRS173539Methylome dataBIGWIG43.61 MB2012-06-27
SAMPLE:SRS173539Methylome dataBIGWIG52.99 MB2012-06-27
SAMPLE:SRS173539Methylome dataBIGWIG43.64 MB2012-06-27
SAMPLE:SRS173540Methylome dataBIGWIG35.69 MB2012-06-27
SAMPLE:SRS173540Methylome dataBIGWIG43.41 MB2012-06-27
SAMPLE:SRS173540Methylome dataBIGWIG35.59 MB2012-06-27
SAMPLE:SRS173541Methylome dataBIGWIG38.84 MB2012-06-27
SAMPLE:SRS173541Methylome dataBIGWIG47.12 MB2012-06-27
SAMPLE:SRS173541Methylome dataBIGWIG38.69 MB2012-06-27
Displaying 1-10 of 283 File(s).

Other datasets you might like: