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Series GSE66144 Query DataSets for GSE66144
Status Public on Sep 07, 2015
Title Bisulfite-free and Base-resolution Analysis of 5-formylcytosine at Whole-genome Scale
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Active DNA demethylation in mammals involves TET-mediated oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxycytosine (5caC). However, genome-wide detection of 5fC at single-base resolution remains challenging. Here we present a bisulfite-free method for the whole-genome analysis of 5fC, based on a selective chemical labeling of 5fC and subsequent C-to-T transition during PCR. Base-resolution 5fC maps reveal limited overlap with 5hmC, with 5fC-marked regions more active than 5hmC-marked ones.
Overall design Utilization of cyclization-enabled C-to-T transition of 5fC (hence “fC-CET”) to obtain genome-wide map of 5fC at single-base resolution
WT and TdgKO mES cell lines. Two non-enriched input DNAs (Input: preAI), two AI labeled samples (Input: AI), two pull-down output samples.
Contributor(s) Xia B, Han D, Lu X, He C, Yi C
Citation(s) 26344045
Submission date Feb 20, 2015
Last update date May 15, 2019
Contact name Dali Han
Organization name University of Chicago
Department Department of Chemisty
Street address 5801 South Ellis Avenue
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (12)
GSM1615104 KO1_AI
GSM1615105 KO1_Output
GSM1615106 KO1_preAI
BioProject PRJNA275968
SRA SRP055375

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

Supplementary file Size Download File type/resource
GSE66144_RAW.tar 647.6 Mb (http)(custom) TAR (of BEDGRAPH)
GSE66144_TDGKO_5fC_mESC_sites.txt.gz 1023.0 Kb (ftp)(http) TXT
GSE66144_WT_5fC_mESC_sites.txt.gz 247.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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