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| Status |
Public on Jan 22, 2015 |
| Title |
TKO_DNMT3B1_bisulfite_hiseq2000 |
| Sample type |
SRA |
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| Source name |
embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic stem cells
genotype: DNMT1,3a,3b-triple-null
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| Growth protocol |
DNMT1,3a,3b-triple-null embryonic stem cells (Tsumura et al., 2006), were cultivated on feeder cells or 0.2% gelatine coated dishes. ES cell growth medium consisted of DMEM (Invitrogen) supplemented with 15% foetal calf serum (Invitrogen), 1x non-essential amino acids (Invitrogen), 1mM L-glutamine, LIF and 0.001% beta-mercaptoethanol. Differentiation was performed as previously described (Bibel et al).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using Proteinase K digest followed by phenol extraction and ethanol precipitation, followed by RNase treatment. Genomic DNA was sonicated using a Bioruptor (7 cycles) to 200-500 bp. Fragmented, pre-methylated phage T7 DNA and unmethylated lambda DNA were spiked in as converson control.
6 ug DNA were end-repaired, poly-adenylated and ligated to methylated, paired-end adapters from Illumina. Ligated DNA fragments were purified on 2% agarose gels. Fragmetns between 350-400bp were extracted and bisulfite conversion was performed using the Qiagen Epitect bisulfite kit. Converted DNA was amplified for 10 cycles and cleaned up with Ampure beads.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina MiSeq |
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| Data processing |
fastq files from MiSeq and HiSeq experiments were pooled and split to 50bp length
fastq files were directly processed and mapped using standard settings for single-end bisulfite sequencing in QuasR in R (http://www.bioconductor.org/packages/release/bioc/html/QuasR.html)
methylation values were extracted with QuasR.
Genome_build: mm9
Supplementary_files_format_and_content: tab-separated values: chr, CG_start, CG_end, tot_reads_TK_D3A2, meth_read_TK_D3A2, tot_reads_TK_D3B1, meth_read_TK_D3B1
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| Submission date |
May 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Dirk Schuebeler |
| Organization name |
Friedrich Miescher Institute for Biomedical Research
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| Street address |
Maulbeerstrasse 66
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| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
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| Platform ID |
GPL16417 |
| Series (2) |
| GSE57411 |
Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation [Bisulfite-Seq] |
| GSE57413 |
Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation |
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| Relations |
| BioSample |
SAMN02767314 |
| SRA |
SRX535248 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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