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Series GSE70519 Query DataSets for GSE70519
Status Public on Jul 05, 2016
Title DNA Cytosine Hydroxymethylation Levels Are Distinct Among Peripheral Blood Leukocytes
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary Peripheral blood leukocytes are the most commonly used surrogates to study epigenome-induced risk and epigenomic response to disease related stress. We considered the hypothesis that the TET enzyme catalyzed hydroxymethylation of 5mC to 5hmC might vary among peripheral blood leukocytes and reflect their responsiveness to environment. Reduction in TET1 and/or TET2 activity leads to the over-proliferation of various leukocyte precursors in bone marrow and acute leukemia, yet, the role of 5mC hydroxymethylation in peripheral blood is less well studied. We developed simplified protocols to rapidly and reiteratively isolate mostly non-overlapping leukocyte populations from a single small sample of fresh or frozen whole blood. Among peripheral leukocyte types we found extreme variation in the levels of transcripts encoding proteins involved in cytosine methylation (DNMT1, 3A, 3B) and turnover by de-methylation (TET1, 2, 3) and DNA repair (GADD45a, b, g) and in the gene-region-specific levels of DNA 5hmC (CD4 T cells >> CD14 monocytes > CD16 neutrophils > CD19 B cells > CD56 NK cells > Siglec 8 eosinophils > CD8 T cells). Taken together our results suggest a hierarchy of responsiveness among classes of leukocytes with CD4+ and CD8+ T cells and CD14 monocytes being the most distinctly potentiated for a rapid methylome response to physiological stress and disease.
Overall design TAB-seq data on 5-hydroxymehtylcytosine (Yu, M. et al. 2012. Cell 149, 1368-1380.) was collected from seven leukocyte types (CD4+ T cells, CD8+ T cells, CD14+ monocytes, CD16+ neutrophils, CD19+ B cells, CD56+ natural killer cells, and Siglec-8+ eosinophils) reiteratively isolated from peripheral blood collected from a healthy male.
Contributor(s) Schmitz RJ
Citation(s) 27164004
Submission date Jul 06, 2015
Last update date May 15, 2019
Contact name Robert J Schmitz
Organization name University of Georgia
Department Genetics
Street address B416 Davison Life Sciences
City Athens
State/province GA
ZIP/Postal code 30602
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (7)
GSM1808328 CD4+ T cell
GSM1808329 CD8+ T cell
GSM1808330 CD14+ monocyte
BioProject PRJNA288943
SRA SRP060353

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Supplementary file Size Download File type/resource
GSE70519_RAW.tar 5.9 Gb (http)(custom) TAR (of TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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