|
| Status |
Public on Aug 15, 2017 |
| Title |
seed following 48 h of stratification (S) Replicate 3 [methylC-seq] |
| Sample type |
SRA |
| |
|
| Source name |
seed following 48 h of stratification (S)
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col0
genotype/variation: wild type
tissue: germinating seed
time point: seed during stratification 48 h S
|
| Treatment protocol |
Samples were collected 48 h into dark stratification started at 4 °C.
Seed was collected freshly harvested (H), after 14 days of drying (0 h), 1, 12 and 48 h during stratification and 1, 6, 12, 24, 48 h in continuous light.
|
| Growth protocol |
Seeds were sown on MS media, statified at 4 C for 2-d before being transferred to continious light at 22C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was extracted from the seeds/seedlings using the Qiagen DNeasy Plant minikit and 600ng of purified gDNA was used for MethylC-seq library preparation after spiking in 0.5% lambda DNA (N6-methyladenine-free) (New England BioLabs).
MethylC-seq library preparation was carried out as described previously (Urich et al., 2015 - http://www.nature.com/nprot/journal/v10/n3/full/nprot.2014.114.html).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
48hS_3
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and filtered for low-quality sequence, with Trim Galore v0.4.2
filered and trimmed reads were mapped with bismark v0.16.3 with default parameters
Deduplicated reads (deduplicate_bismark) were used to generate genome-wide cytosine reports (bismark_methylation_extractor, bismark2bedGraph, coverage2cytosine)
DMRs were identified using HOME (hten used to identify timeseries DMRs for three context CG, CHG and CHH using HOME-timeseries with default parameters. We further filtered out regions whose maximum absolute difference in methylation during the timecourse was lower than 20%.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited files including genome-wide cytosine report, and bed files of unfiltered DMRs in CG, CHG and CHH contexts.
|
| |
|
| Submission date |
Feb 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Quentin Gouil |
| Organization name |
Olivia Newton-John Cancer Research Institute
|
| Lab |
Health and Epigenomics Across Life
|
| Street address |
Studley Road
|
| City |
Heidelberg |
| State/province |
VIC |
| ZIP/Postal code |
3085 |
| Country |
Australia |
| |
|
| Platform ID |
GPL17311 |
| Series (2) |
| GSE94456 |
methylC-seq data over Arabidopsis thaliana germination |
| GSE94459 |
methylC-seq, RNA-seq and sRNA-seq data over Arabidopsis thaliana germination |
|
| Relations |
| BioSample |
SAMN06293564 |
| SRA |
SRX2536470 |
