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| Status |
Public on Feb 02, 2017 |
| Title |
MKS_322K_RRBS |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
genotype: MAT1A KO
age: 10 month
treatment: SAMe supplementation
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| Growth protocol |
Mice were breed and housed at the Animal Facility of CIC bioGUNE under controled conditions according to the animal care international gidelines.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from the livers using AllPrep DNA/RNA Mini Kit
RRBS/MspI+TaqαI, followed by a modified NEXTflex™ Bisulfite-Seq Kit (Illumina Compatible, Bioo Scientific Corp Catalog #5119-01). Samples were multiplexed according to Illumina's recommendations and experimental design.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiScanSQ |
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| Data processing |
Basecalls performed using CASAVA version 1.8.2
Individual FASTQ files for each sample were merged prior to the quality control & filtering steps
Reads were filtered from the adapter sequences and their quality score using trim_galore software. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and only are retained those with at least 20 phred quality score.
Reads were mapped to mm10 (Mus musculus) reference genome using the Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) allowing two alignment mismatches (n 2).
Resulting SAM aligment files were sorted to be used in as input in further steps.
In order to call methylation score for a base position, we required that read bases aligning to that position have at least 5X coverage. We use methylKit to compute methylation ratios and differential methylation analysis (http://code.google.com/p/methylkit/)
Genome_build: mm10
Supplementary_files_format_and_content: Differentially methylated regions (DMR) table obtained from Methylkit processing of the SAM files yieldedby Bismark alignment. Each table representes the following parameters: Chromosome (chr), start and end coordinates of the methylated region (start, end), strand location (strand), probability value "pvalue", adjusted p-value "qvalue", differential methylation score "meth.diff". Only regions with a meth.diff score over 20 or under -20, and a qvalue under 0.05, where considered as differentially methylated (Hyper- or Hypo- methylated respectively).
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| Submission date |
Jan 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jose Luis Lavin |
| E-mail(s) |
joluito@gmail.com
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| Organization name |
CIC bioGUNE
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| Street address |
Parque Tecnológico de Bizkaia Building 502, Floor 0
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| City |
Derio |
| State/province |
Bizkaia |
| ZIP/Postal code |
48160 |
| Country |
Spain |
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| Platform ID |
GPL16173 |
| Series (2) |
| GSE77079 |
DNA methylation status of the liver of MAT1A WT and MAT1A KO mice treated with placebo or SAMe during 8 weeks |
| GSE77084 |
Liver of MAT1A WT and MAT1A KO mice treated with placebo or SAMe during 8 weeks |
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| Relations |
| BioSample |
SAMN04432779 |
| SRA |
SRX1539714 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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