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Sample GSM1162046 Query DataSets for GSM1162046
Status Public on Jun 03, 2014
Title methyl-C-seq_DKO_rep1
Sample type SRA
Source name mouse embryonic stem cells
Organism Mus musculus
Characteristics cell type: mouse embryonic stem cells
genotype: Dnmt3a/3b DKO
Growth protocol mESCs were grown in DMEM supplemented with 15% FBS (HyClone), 20 mM Hepes, 0.1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol, 100 U/mL penicillin, 0.05 mM streptomycin, leukemia inhibitory factor (1000 U/ml), and 2 mM glutamine.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from mESCs and was spiked in with unmethylated lambda DNA (Promega). The DNA was fragmented by sonication.
The DNA was fragmented by sonication. Purified DNA fragments were end-repaired. After A-tailing reaction, fragments were ligated to paired-end cytosine-methylated adapters provided by Illumina. Size-selected adaptor-ligated DNA was treated with sodium bisulfite using the EZ DNA methylation-Gold Kit (Zymo Research). The resulting DNA molecules were enriched by PCR, purified, and sequenced following standard protocols from Illumina.
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina Genome Analyzer IIx
Description bisulfite-converted genomic DNA
Data processing Basecalls performed using CASAVA version 1.4
MethylC-Seq reads were mapped as previously described (Lister et al., Nature, 2009). Briefly, reads were trimmed until encountering a base with PHRED score <= 2 and bases near the 3' end were trimmed if the adapter sequence was included. For the purpose of mapping, all cytosines were computationally converted to thymines, to be reverted back to their original state after mapping. The Bowtie program(Langmead et al. 2009) was then used to align these computationally converted reads to computationally converted copies of hg18. Non-uniquely mapping reads were discarded
Non-monoclonal reads were filtered out using the Picard software
Using the Samtools Pileup command, for each genomic position the number of reads with match and mismatch were counted in a strand sepcific manner, more specifically, the number of methylated and non-methylated reads per CpG were determined. Individual bases with Phred score < 20 were filtered out. The genome was then divided up into bins of 100 bp and the CpG methylation ratio was calculated by capturing the number of methylated CpG reads in comparison to all reads at CpG for each bin by combining the two replicates and by combining plus- and minus-strand. The methylation ratios per 100bp were used to compose bigwig files.
Genome_build: mm9
Submission date Jun 12, 2013
Last update date May 15, 2019
Contact name Ulrich Wagner
Organization name Uiversity Hospital Zurich
Street address Schmelzbergstrasse 12
City Zurich
ZIP/Postal code 8091
Country Switzerland
Platform ID GPL11002
Series (2)
GSE47893 Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases (Dnmt3ab KO Methyl-Seq)
GSE47894 Maintenance of DNA methylation in embryonic stem cells depends on the histone H3K9 methyltransferases
BioSample SAMN02202326
SRA SRX305019

Supplementary file Size Download File type/resource 80.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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