 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 07, 2020 |
| Title |
Extraction and high-throughput sequencing of oak heartwood DNA: assessing the feasibility of genome-wide DNA methylation profiling |
| Organism |
Quercus robur |
| Experiment type |
Methylation profiling by high throughput sequencing
Other
|
| Summary |
Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability particularly of oak heartwood and, hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies in the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. We investigated the feasibility of such studies using heartwood samples core-drilled from the trunks of standing oak trees spanning the AD 1776-2014. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. We sequenced whole-genome and DNA methylome libraries for oak heartwood up to 100 and 50 years of age, respectively. However, only 56 genomic regions with sufficient coverage for quantitative methylation analysis were identified, suggesting that the high-throughput sequencing of DNA will be in principal feasible for wood formed <100 years ago is impeded by the reduction in library complexity caused by the bisulfite treatment used to generate the oak methylome.
|
| |
|
| Overall design |
Examination of whole-genome sequencing in 12 oak (Quercus robur) wood samples (4 sapwood, 8 heartwood) from 4 trees and whole-genome bisulfite sequencing in 4 oak (Quercus robur) wood samples (2 sapwood, 2 heartwood) from 2 trees
|
| |
|
| Contributor(s) |
Rossi F, Crnjar A, Comitani F, Feliciano R, Jah L, Malim G, Southgate L, Kay E, Oakey R, Buggs R, Moir A, Kistler L, Rodriguez Mateos A, Molteni C, Schulz R |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Jan 06, 2020 |
| Last update date |
Jan 09, 2020 |
| Contact name |
Federico Rossi |
| E-mail(s) |
federico.rossi@ieo.it
|
| Organization name |
Istituto Europeo Oncologia
|
| Street address |
Via Adamello 16
|
| City |
Milan |
| ZIP/Postal code |
10142 |
| Country |
Italy |
| |
|
| Platforms (1) |
|
| Samples (19)
|
|
| Relations |
| BioProject |
PRJNA599186 |
| SRA |
SRP239605 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE143201_RAW.tar |
30.8 Mb |
(http)(custom) |
TAR (of COV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...