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Status |
Public on Nov 17, 2013 |
Title |
Large conserved domains of low DNA methylation maintained by 5-hydroxymethycytosine and Dnmt3a [Bisulfite-Seq] |
Organism |
Mus musculus |
Experiment type |
Methylation profiling by high throughput sequencing
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Summary |
Gains and losses in DNA methylation are prominent genomic features of all mammalian cell types. To gain insight into mechanisms that could promote shifts in DNA methylation patterns and thus contribute to cell fate, including malignant transformation, we performed genome-wide mapping of 5-methylcytosine in purified wild type and Dnmt3a conditional knockout hematopoietic stem cells (HSCs). We generated 1,121 million (control HSCs), and 1,213 million (Dnmt3a knockout HSCs) raw reads; about 81.4% and 88.7%, respectively, were successfully aligned to either strand of the reference genome (mm9), obtainig an average CG coverage of 39.5-fold (wild type) and 47.0-fold (Dnmt3a kockout).
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Overall design |
Whole genome bisulfite sequencing of secondarily-transplanted wild-type and Dnmt3a conditional knockout hematopoietic stem cells using Illumina HiSeq 2000
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Contributor(s) |
Rodriguez B, Li W, Goodell M |
Citation(s) |
24270360 |
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Submission date |
Aug 10, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Margaret Goodell |
Organization name |
Baylor College of Medicine
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Street address |
One Baylor Plaza, N1030
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City |
Houston |
State/province |
TX |
ZIP/Postal code |
77030 |
Country |
USA |
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Platforms (1) |
GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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Samples (16)
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This SubSeries is part of SuperSeries: |
GSE49191 |
Large conserved domains of low DNA methylation maintained by 5-hydroxymethycytosine and Dnmt3a |
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Relations |
BioProject |
PRJNA214817 |
SRA |
SRP028709 |