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| Status |
Public on Jun 20, 2013 |
| Title |
Liver rrbs mmu lv m |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
Sex: male
tissue: Liver
strain: C57BL/6
age: 11 weeks
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
see Smith et al. 2009 and Bernstein et al. 2005
For RRBS, two sets of DNA methylation bisulfite sequencing libraries (differing by their insert sizes) were generated, using a previously described protocol (Smith et al. 2009), for the 5 mouse samples (brain, liver, testis, spermatocyte and spermatid). These libraries were sequenced (38 and 76 cycles, respectively) on the Illumina Genome Analyzer IIx platform, yielding a total of ∼322 million reads (mean of ∼64 million reads per sample). For ChIP-seq, Chromatin immunoprecipitation with antibodies against H3K4me2 was carried out as previously described (Bernstein et al. 2005), for the same samples for which DNA methylation data were produced. Sequencing libraries were prepared according to the Illumina protocol for ChIP sequencing and sequenced (38 cycles) using the Illumina Genome Analyzer IIx platform, yielding a total of ∼131 million reads (mean: ∼26 million reads per sample).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
In house, C57BL7/6 colonies
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| Data processing |
The basecalling was performed with Ibis (Kircher et al, 2009). The quality values are given in the phred-33 format, for all samples.
RRBS reads were mapped onto the mouse genome using the BSMAP mapping tool, which was specifically designed for bisulfite sequence mapping (Xi and Li 2009). Percentages of DNA methylation levels based on bisulfite conversation yield were computed at the single nucleotide scale for positions represented by at least 10X coverage of uniquely mapped reads.
Reads were mapped onto the mouse genome using Bowtie (Langmead et al. 2009). We then determined the coverage per base for each sample by restricting our data to 16 million randomly resampled uniquely mapped reads.
Genome_build: mm9
Supplementary_files_format_and_content: *MethylationCount.tab is a tab delimited file containing DNA methylation levels based on bisulfite conversation at the single nucleotide scale for positions represented by at least 10X of coverage. *.cov is a tab delimited file containing the coverage per base for each sample by restricting our data to 16 million randomly resampled uniquely mapped reads.
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| Submission date |
Jan 24, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Magali Soumillon |
| E-mail(s) |
mag.soumillon@gmail.com
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| Organization name |
Harvard University, HSCRB
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| Street address |
Divinity Avenue 7
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
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| Platform ID |
GPL11002 |
| Series (1) |
| GSE43719 |
Cellular source and mechanisms of high transcriptome complexity in the mammalian testis (RRBS and ChIP-Seq) |
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| Relations |
| SRA |
SRX219249 |
| BioSample |
SAMN01894397 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1069660_mmu_lv_m_MethylationCount.tab.txt.gz |
63.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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