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| Status |
Public on Nov 14, 2014 |
| Title |
RRBS E6.5 |
| Sample type |
SRA |
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| Source name |
E6.5 epiblasts
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| Organism |
Mus musculus |
| Characteristics |
embryo stage: E6.5
gender: mixed
genotype/variation: WT
strain: C57BL/6J
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted by proteinase K digestion followed by phenol/chloroform extraction.
We prepared RRBS libraries using a published protocol (Gu et al., Nat Protoc 6:468-81, 2011) with some modifications. Briefly, we digested 25-100 ng of genomic DNA 5 hours with MspI (Fermentas), followed by end-repair and A-tailing (Klenow fragment, Fermentas), and ligation to methylated adapters (T4 DNA ligase, Fermentas) in Tango 1X buffer. Fragments between 150 and 400 bp were excised from a 3% agarose 0.5X TBE gel with the MinElute kit (Qiagen) and bisulfite-converted with the EpiTect Bisulfite kit (Qiagen) using two consecutive rounds of conversion. Final RRBS libraries were amplified with 14-16 cycles of PCR.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
We cleaned sequencing reads with Trim Galore v0.2.1 using the parameters --rrbs --paired -r1 30 -r2 30 -q 20 --length 20 --retain_unpaired.
We aligned to the mouse mm10 genome with BSMAP v2.74 using the parameters -v 2 -w 100 -r 1 -x 400 -m 30 -D C-CGG -n 1.
We extracted methylation percent values as the ratio of the number of Cs over the total number of Cs and Ts with methratio.py from BSMAP v2.74 using the parameters -z -u -g.
We then filtered CGs to have a minimum sequencing depth of 8x using custom developped scripts in R v3.0.0.
Genome_build: mm10
Supplementary_files_format_and_content: We provide .igv files containing methylation scores calculated for all CGs with at least 8x sequencing depth.
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| Submission date |
Aug 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Weber |
| Organization name |
CNRS
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| Department |
UMR7242 Biotechnology and Cell Signalling
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| Street address |
300 Bd Sebastien Brant
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| City |
Illkirch |
| ZIP/Postal code |
67412 |
| Country |
France |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE60334 |
DNA methylation analysis and expression profiling during murine embryogenesis and in embryos deficient for DNMT3A or DNMT3B |
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| Relations |
| BioSample |
SAMN02983100 |
| SRA |
SRX675916 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1471899_RRBS_E6.5.igv.gz |
8.3 Mb |
(ftp)(http) |
IGV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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