 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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 |
| E-mail(s) |
schmitz@uga.edu
|
| 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)
|
|
| Relations |
| BioProject |
PRJNA288943 |
| SRA |
SRP060353 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE70519_RAW.tar |
5.9 Gb |
(http)(custom) |
TAR (of TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...