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Series GSE214006 Query DataSets for GSE214006
Status Public on Mar 15, 2023
Title Modular oxidation of cytosine modifications and their application in direct and quantitative sequencing of 5-hydroxymethylcytosine
Organisms Homo sapiens; Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Selective, efficient, and controllable oxidation of cytosine modifications is valuable for epigenetic analyses, yet only limited progress has been made. Here, we present two modular chemical oxidation reactions: conversion of 5-hydroxymethylcytosine (5hmC) into 5-formylcytosine (5fC) utilizing 4-acetamido-2,2,6,6-tetramethylpiperidine-1-oxoammonium tetrafluoroborate (ACT+ BF4–) and further transformation of 5fC into 5-carboxycytosine (5caC) through Pinnick oxidation. Both reactions are mild and efficient on double-stranded DNA. We integrated these two oxidations with borane reduction to develop chemical-assisted pyridine borane sequencing plus (CAPS+), for direct and quantitative mapping of 5hmC. Compared with chemical-assisted pyridine borane sequencing (CAPS), CAPS+ improved the conversion rate and false-positive rate. We applied CAPS+ to mouse embryonic stem cells (mESCs) DNA, human normal brain and glioblastoma DNA samples, and demonstrated its superior sensitivity in analyzing the hydroxymethylome
Overall design Whole genome sequencing of 5 hydroxymethylcytosine applying CAPS+ in mESCs (two replicates) and human brain samples (normal brain and glioblastoma).
Contributor(s) Xu H, Chen J, Cheng J, Kong L, Chen X, Inoue M, Liu Y, Zhao M, Song C
Citation(s) 36961225
Submission date Sep 23, 2022
Last update date May 02, 2023
Contact name Linzhen Kong
Organization name Ludwig Institute for Cancer Research
Department Nuffield Department of Medicine
Lab Dr. Chunxiao Song's group
Street address University of Oxford Old Road Campus Research Building
City Oxford
ZIP/Postal code OX3 7FZ
Country United Kingdom
Platforms (2)
GPL30172 NextSeq 2000 (Mus musculus)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (4)
GSM6597700 E14 mESC, CAPS+, rep1
GSM6597701 E14 mESC, CAPS+, rep2
GSM6597702 normal brain, CAPS+
BioProject PRJNA883609

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Supplementary file Size Download File type/resource
GSE214006_brain_healthy_astair_CpG.filtered.bedGraph.gz 362.6 Mb (ftp)(http) BEDGRAPH
GSE214006_brain_tumor_astair_CpG.filtered.bedGraph.gz 329.5 Mb (ftp)(http) BEDGRAPH
GSE214006_mESC_merged_astair_CpG_filtered.bedGraph.gz 255.0 Mb (ftp)(http) BEDGRAPH
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