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Series GSE130556 Query DataSets for GSE130556
Status Public on Jun 04, 2021
Title Identifying subpopulation methylation profiles from sequencing of heterogeneous samples with DXM
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary Changes in epigenetic marks, such as DNA methylation, in cancer subclones may increase their fitness, leading to cancer progression, treatment resistance, and worse prognosis. We have developed DXM, a novel computational method to identify subpopulation methylation events from bisulfite sequencing data of a heterogeneous sample
DXM does not require prior knowledge of the number of cell types or what cell types to expect in the sample, and it outperforms existing methods.
To further validate our method, we conducted genomic bisulfite sequencing on four primary DLBCL samples, obtaining data from >4.9 million CpGs at 50x average coverage.
DXM predictions of subpopulation methylation profiles in these samples were confirmed in FACS-sorted CD4+ and CD19+ cells.
Thus, we have developed a method, DXM, that can identify subpopulation methylation profiles in heterogeneous samples
Overall design Bisulfite Sequencing (Agilent Methyl-Seq) of four cryopreserved primary DLBCL samples
Citation(s) 34157105
Submission date May 01, 2019
Last update date Sep 24, 2021
Contact name Jerry Fong
Organization name Washington University School of Medicine
Street address 4565 McKinley Ave
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (4)
GSM3743484 DLBCL, methylSeq_1
GSM3743485 DLBCL, methylSeq_2
GSM3743486 DLBCL, methylSeq_3
BioProject PRJNA540605
SRA SRP194373

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
GSE130556_RAW.tar 149.5 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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