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Sample GSM2476054 Query DataSets for GSM2476054
Status Public on Aug 15, 2017
Title seed collected 6 h into countinuous light (post-stratification), 6 h SL Replicate 3 [methylC-seq]
Sample type SRA
 
Source name seed collected 6 h into countinuous light (post-stratification), 6 h SL
Organism Arabidopsis thaliana
Characteristics ecotype: Col0
genotype/variation: wild type
tissue: germinating seed
time point: seed germinating in countinuous light 6 h SL
Treatment protocol Following 48 h of cold, dark stratification (4 °C), samples were transferred into light conditions (100 µE m -2 sec-1) at 22 °C and collected after 6h.
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 6hSL_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 Walter and Eliza Hall
Department Epigenetics and Development
Lab Ritchie lab
Street address 1G Royal Parade
City Parkville
State/province VIC
ZIP/Postal code 3052
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 SAMN06293563
SRA SRX2536473

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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