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Series GSE128560 Query DataSets for GSE128560
Status Public on Aug 14, 2019
Title DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary Genome-wide profiling of copy number alterations and DNA methylation in single cells could enable detailed investigation into the genomic and epigenomic heterogeneity of tumor populations. However, current methods to do this require complex sample processing and cleanup steps, lack consistency, or are biased in their genomic representation. Here, we describe a novel single-tube enzymatic method, DNA Analysis by Restriction Enzyme (DARE), to perform deterministic whole genome amplification while preserving DNA methylation information. This method was evaluated on low amounts of DNA and single cells, and provides accurate copy number aberration calling and representative DNA methylation measurement across the whole genome. Single cell DARE is an attractive and scalable approach for concurrent genomic and epigenomic characterization of cells in a heterogeneous population.
Overall design Analysis of HepG2 and K562 copy number aberrations and methylation status in bulk genomic DNA and single cells. ESC bulk genomic DNA was used to verify the copy number aberration analysis.
Contributor(s) Cheow LF, Viswanathan R, Cheruba E
Citation(s) 31418018
Submission date Mar 19, 2019
Last update date Nov 12, 2019
Contact name Lih Feng Cheow
Organization name National University of Singapore
Department Biomedical Engineering
Lab Technology Innovations for Systems Biology
Street address 4 Engineering Drive 3
City Singapore
ZIP/Postal code 117583
Country Singapore
Platforms (2)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (29)
GSM3680079 HepG2_100ng_1
GSM3680080 HepG2_100ng_2
GSM3680081 HepG2_1ng_1
BioProject PRJNA528100
SRA SRP188880

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Supplementary file Size Download File type/resource
GSE128560_RAW.tar 151.5 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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