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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
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 Bo He
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
BioProject PRJNA439006
SRA SRP136030

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

Supplementary file Size Download File type/resource 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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