|
Status |
Public on Sep 01, 2017 |
Title |
Genome-wide single-molecule sequencing of 6-methyladenine in eukaryotes |
Organisms |
Chlamydomonas reinhardtii; Arabidopsis thaliana; Saccharomyces cerevisiae; Caenorhabditis elegans; Drosophila melanogaster; Nannochloropsis oceanica; Auricularia delicata |
Experiment type |
Methylation profiling by high throughput sequencing Third-party reanalysis
|
Summary |
Mapping 6mA at single-base resolution across multiple eukaryotic genomes reveals its genomic distribution patterns, indicating a function in transcriptional regulation.
|
|
|
Overall design |
Using genome-wide methylation detection by single-molecule sequencing, we mapped 6mA at single-base resolution in seven eukaryotic species including the model plant Arabidopsis thaliana, the green alga Chlamydomonas reinhardtii, the marine alga Nannochloropsis oceanica, and the wood-degrading fungus Auricularia delicata. We also performed methylation mapping of publicly available raw SMRT sequencing data from two animal models, Drosophila melanogaster and Caenorhabditis elegans, and budding yeast, Saccharomyces cerevisiae.
|
|
|
Contributor(s) |
Wei C, Ngan CY, Tolkunov D |
Citation missing |
Has this study been published? Please login to update or notify GEO. |
|
Submission date |
May 13, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Denis Tolkunov |
Organization name |
DOE Joint Genome Institute
|
Street address |
2800 Mitchell Dr
|
City |
Walnut Creek |
State/province |
CA |
ZIP/Postal code |
94598 |
Country |
USA |
|
|
Platforms (8)
|
GPL18482 |
Illumina HiSeq 2500 (Chlamydomonas reinhardtii) |
GPL19919 |
PacBio RS II (Caenorhabditis elegans) |
GPL20195 |
PacBio RS II (Chlamydomonas reinhardtii) |
GPL20196 |
PacBio RS (Auricularia delicata) |
GPL20197 |
PacBio RS II (Arabidopsis thaliana) |
GPL20198 |
PacBio RS II (Nannochloropsis oceanica) |
GPL20199 |
PacBio RS II (Drosophila melanogaster) |
GPL20200 |
PacBio RS II (Saccharomyces cerevisiae) |
|
Samples (11)
|
GSM1684587 |
Chlamydomonas reinhardtii, replicate 1 (4A+, log phase) |
GSM1684588 |
Chlamydomonas reinhardtii, replicate 2 (4A+, log phase) |
GSM1684589 |
Chlamydomonas reinhardtii, replicate 3 (4A+, log phase) |
GSM1684590 |
Chlamydomonas reinhardtii, replicate 1 (4A+, 48h post Nitrogen depletion) |
GSM1684591 |
Chlamydomonas reinhardtii, replicate 2 (4A+, 48h post Nitrogen depletion) |
GSM1684592 |
Auricularia delicata (TFB10046 SS-5) |
GSM1684593 |
Arabidopsis thaliana (Col-0, 11 days) |
GSM1684594 |
Nannochloropsis oceanica (IMET1, log phase) |
GSM1684595 |
Drosophila melanogaster |
GSM1684596 |
Caenorhabditis elegans |
GSM1684597 |
Saccharomyces cerevisiae |
|
Relations |
BioProject |
PRJNA283916 |
SRA |
SRP058325 |