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Series GSE41060 Query DataSets for GSE41060
Status Public on Sep 26, 2012
Title Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax.
Organism Oxytricha trifallax
Experiment type Methylation profiling by high throughput sequencing
Summary We report the existence of both methylcytosine and hydroxymethylcytosine in the genomic DNA of the ciliate Oxytricha trifallax during its genome rearrangement process. These modifications are dynamically added, de novo, to sequences targeted for elimination and are not present after the rearrangement process (in vegetative cells). We performed methyl-DNA immunoprecipitation-sequencing (meDIP-seq) with antibodies against methylcytosine and hydroxymethylcytosine.
 
Overall design We performed methyl-DNA immunoprecipitation-sequencing (meDIP-seq) with antibodies against methylcytosine and hydroxymethylcytosine, and used an IgG control for nonspecific immunoprecpitation. Immunoprecipitation was performed on both vegetative (negative control) and 46h cells (with methylation). The data were normalized to RPKM, then the number of vegetative reads was subtracted from the number of 46h reads, giving excess reads at 46h, which we denote as the methylation/hydroxymethylation "signal". Those data are reported in the tab-deliminated data files included with this dataset.
 
Contributor(s) Bracht JR, Perlman DH, Landweber LF
Citation(s) 23075511
Submission date Sep 21, 2012
Last update date May 15, 2019
Contact name John Russell Bracht
Organization name Princeton University
Street address Washington Rd. Guyot Hall rm 323
City Princeton
State/province NJ
ZIP/Postal code 08544
Country USA
 
Platforms (1)
GPL15459 Illumina HiSeq 2000 (Oxytricha trifallax)
Samples (6)
GSM1008119 Vegetative IgG DIP-seq
GSM1008120 Vegetative mC DIP-seq
GSM1008121 Vegetative hmC DIP-seq
Relations
BioProject PRJNA175642
SRA SRP015837

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Supplementary file Size Download File type/resource
GSE41060_MAC_IgG_mC_hmC_subtracted.txt.gz 99.7 Kb (ftp)(http) TXT
GSE41060_MIC_IgG_mC_hmC_subtracted.txt.gz 605 b (ftp)(http) TXT
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Processed data are available on Series record

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