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Series GSE112048 Query DataSets for GSE112048
Status Public on Oct 09, 2018
Title Bisulfite-free, nano-scale analysis of 5-hydroxymethylcytosine at single base resolution
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Other
Summary High-resolution detection of genome-wide 5-hydroxymethylcytosine (5hmC) sites of small-scale samples represents a continuous challenge. Here, we present CATCH-seq, a bisulfite-free, base-resolution method for the genome-wide detection of 5hmC. CATCH-seq is based on selective 5hmC oxidation, labeling and subsequent C-to-T transition during PCR. Applications of CATCH-seq to nano-scale DNA samples reveal previously underappreciated non-CG 5hmCs in the hESC genome and base-resolution hydroxymethylome in human cell-free DNA.
 
Overall design We developed a method named "CATCH-Seq" , a bisulfite-free, base-resolution method for the genome-wide detection of 5hmC. Our method is based on: (1) selective oxidation of 5hmC to 5fC ; (2) subsequent labeling of the newly generated 5fC; and (3) 5fC labeling adduct caused C-to-T transition during DNA amplification.We then applied CATCH-seq to 100 ng, 50 ng and 10 ng genomic DNA isolated from hESCs, respectively. To further demonstrate the utility of CATCH-seq in analyzing precious clinical samples, we next applied this approach to sequence the hydroxymethylome of cell-free DNA (cfDNA).
 
Contributor(s) Zeng H, He B, Xia B, Yi C
Citation(s) 30278133
Submission date Mar 19, 2018
Last update date Mar 27, 2019
Contact name Chengqi Yi
E-mail(s) chengqi.yi@pku.edu.cn
Organization name Peking University
Department School of Life Science
Street address Yiheyuan Road 5th.
City Beijing
State/province Beijing
ZIP/Postal code 100871
Country China
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (18)
GSM3053816 hESC_100ng_rep1_input
GSM3053817 hESC_100ng_rep1_output
GSM3053818 hESC_100ng_rep2_input
Relations
BioProject PRJNA439006
SRA SRP136030

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
GSE112048_H1_ESCs.hg19.5hmC.site.txt.gz 2.2 Mb (ftp)(http) TXT
GSE112048_RAW.tar 508.4 Mb (http)(custom) TAR (of BED, BW)
GSE112048_gene_list.txt.gz 9.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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