|
| 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.
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| |
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| 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://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-0943-7
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| |
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| 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) |
[email protected]
|
| 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] |
| GSM2059595 |
Genomic DNA from a reconstructed mixture of purified human leukocytes [9985131146_R02C01] |
| GSM2059596 |
Genomic DNA from a reconstructed mixture of purified human leukocytes [9985131137_R04C02] |
| GSM2059597 |
Genomic DNA from a reconstructed mixture of purified human leukocytes [9985131146_R05C01] |
| GSM2059598 |
Genomic DNA from a reconstructed mixture of purified human leukocytes [9985131146_R06C01] |
| GSM2059599 |
Genomic DNA from a reconstructed mixture of purified human leukocytes [9985131145_R06C02] |
| GSM2059600 |
Genomic DNA from a reconstructed mixture of purified human leukocytes [9985131146_R01C02] |
| GSM2059601 |
Genomic DNA from a reconstructed mixture of purified human leukocytes [9985131137_R04C01] |
| GSM2059602 |
Genomic DNA from a reconstructed mixture of purified human leukocytes [9985131137_R06C02] |
| GSM2059603 |
Genomic DNA from a reconstructed mixture of purified human leukocytes [9985131146_R03C02] |
| GSM2059604 |
Genomic DNA from adult human whole blood [9985131137_R02C02] |
| GSM2059605 |
Genomic DNA from adult human whole blood [9985131137_R05C01] |
| GSM2059606 |
Genomic DNA from adult human whole blood [9985131145_R04C01] |
| GSM2059607 |
Genomic DNA from adult human whole blood [9985131146_R01C01] |
| GSM2059608 |
Genomic DNA from adult human whole blood [9985131146_R03C01] |
| GSM2059609 |
Genomic DNA from adult human whole blood [9985131146_R04C02] |
|
| Relations |
| BioProject |
PRJNA311630 |
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