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Series GSE77797 Query DataSets for GSE77797
Status Public on Feb 12, 2016
Title DNA methylation profiling of whole blood and reconstructed mixtures of purified leukocytes isolated from human adult blood
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Confounding due to cellular heterogeneity represents one of the foremost challenges currently facing Epigenome-Wide Association Studies (EWAS). Statistical methods leveraging the tissue-specificity of DNA methylation for deconvoluting the cellular mixture of heterogeneous biospecimens such as whole blood, offer a promising solution. However, their performance depends entirely on the library of DNA methylation markers being used as the basis for deconvolution. The objective of this study was to train and validate an algorithm for the identification of optimal DNA methylation libraries for the deconvolution of adult human whole blood.
 
Overall design Purified granulocytes, monocytes, CD4T, CD8T, natural killer cells, and B cells from normal human subjects were purchased from AllCells LLC (Emeryville, CA). DNA extracted from purified leukocyte subtypes were mixed in predetermined proportions to reconstruct two distinct sets of white blood cell (WBC) mixtures, each consisting of six samples. An additional six whole blood (WB) samples from disease-free adult donors with available immune cell profiling data from flow cytometry were purchased from All-Cells LLC and were included in this investigation. All DNA samples were bisulfite modified using the Zymo EZ DNA Methylation kit (Irvine, CA) and profiled for DNA methylation using the Illumina HumanMethylation450 array platform.
Web link http://0-bmcbioinformatics-biomedcentral-com.brum.beds.ac.uk/articles/10.1186/s12859-016-0943-7
 
Contributor(s) Koestler DC, Christensen BC, Wiencke JK, Kelsey KT
Citation(s) 26956433, 27965295
Submission date Feb 10, 2016
Last update date Jul 12, 2019
Contact name Devin Charles Koestler
E-mail(s) dkoestler@kumc.edu
Phone 9135884788
Organization name University of Kansas Medical Center
Department Biostatistics
Street address 3901 Rainbow Blvd.
City Kansas City
State/province KS
ZIP/Postal code 66160
Country USA
 
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (18)
GSM2059592 Genomic DNA from a reconstructed mixture of purified human leukocytes [9985131145_R03C02]
GSM2059593 Genomic DNA from a reconstructed mixture of purified human leukocytes [9985131145_R02C01]
GSM2059594 Genomic DNA from a reconstructed mixture of purified human leukocytes [9985131145_R05C01]
Relations
BioProject PRJNA311630

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
GSE77797_RAW.tar 331.5 Mb (http)(custom) TAR (of IDAT)
GSE77797_non-normalized.txt.gz 43.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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