NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE68575 Query DataSets for GSE68575
Status Public on Jan 01, 2016
Title A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways [T-cells]
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary To characterize the largely unknown functions of oxidised methylcytosines (oxi-mC; 5hmC/5fC/5caC) in DNA, several sequencing protocols have been recently developed. Quantitative analysis is complicated because DNA methylation modifications need to be deconvoluted from the data which is affected by several experimental parameters, including e.g. imperfect bisulphite conversion, oxidation efficiencies, various chemical labeling and protection steps, and sequencing errors. Here, we present a hierarchical generative model, Lux, for integrative analysis of any combination of BS-seq and “oxi-mC”-seq (BS-seq/oxBS-seq/TAB-seq/fCAB-seq/CAB-seq/redBS-seq/MAB-seq) data. We show that Lux improves quantification and comparison of methylation levels over existing methods and that Lux can easily process any oxi-mC-seq data sets to quantify all cytosine modifications simultaneously together with their experimental parameters. Application of Lux to targeted data from Tet2 knockdown ESCs and T cells during development demonstrates DNA modification quantification at unprecedented detail, quantifies active demethylation pathway and reveals 5hmC localization in putative regulatory regions.
 
Overall design Examine the distribution of C, 5mC, and 5hmC in DP, CD4 SP, and naïve CD4 T cells within selected loci.
Half of the samples are measured using the traditional bisulphite-seq protocol but the other half is measured using the oxidative bisulphite-seq protocol (oxBS-seq).
 
Contributor(s) Huang Y, Tsagaratou A, Rao A
Citation(s) 26975309
Submission date May 05, 2015
Last update date May 15, 2019
Contact name Tarmo Äijö
Organization name Flatiron Institute
Department Center for Computational Biology
Street address 162 5th Avenue
City New York
ZIP/Postal code 10010
Country USA
 
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (18)
GSM1675791 DP BS-seq replicate 1
GSM1675792 DP BS-seq replicate 2
GSM1675793 DP BS-seq replicate 3
This SubSeries is part of SuperSeries:
GSE68576 A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways
Relations
BioProject PRJNA283129
SRA SRP058012

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
GSE68575_RAW.tar 190.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap