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Series GSE49714 Query DataSets for GSE49714
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
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).
 
Overall design Whole genome bisulfite sequencing of secondarily-transplanted wild-type and Dnmt3a conditional knockout hematopoietic stem cells using Illumina HiSeq 2000
 
Contributor(s) Rodriguez B, Li W, Goodell M
Citation(s) 24270360
Submission date Aug 10, 2013
Last update date May 15, 2019
Contact name Margaret Goodell
Organization name Baylor College of Medicine
Street address One Baylor Plaza, N1030
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (16)
GSM1206254 ko3a_b7l2 Bisulfite-Seq
GSM1206255 ko3a_b7l1 Bisulfite-Seq
GSM1206256 ko3a_b5 Bisulfite-Seq
This SubSeries is part of SuperSeries:
GSE49191 Large conserved domains of low DNA methylation maintained by 5-hydroxymethycytosine and Dnmt3a
Relations
BioProject PRJNA214817
SRA SRP028709

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE49714_RAW.tar 2.4 Gb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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