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Sample GSM3176816 Query DataSets for GSM3176816
Status Public on Jun 11, 2018
Title seeds following 4 d of aerobic germination (4dA) Methyl-Seq Replicate 2
Sample type SRA
Source name Rice coleoptile
Organism Oryza sativa
Characteristics tissue: coleoptile
genotype: WT(Oryza sativa cv Amaroo)
age: seeds following 4 d of aerobic germination (4dA) Replicate 2
treatment/conditions: De-hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30 C in the dark for 4 d.
Treatment protocol For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested.
Growth protocol Rice (Oryza sativa ‘Amaroo’) was de‐hulled, surface sterilised and grown in culture medium [0.5 mm 2‐(N‐morpholine)‐ethanesulphonic acid (MES), 0.4 mm CaSO4, pH 6.5) that was bubbled with air or nitrogen gas (N2) (6–7 L min−1).
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 -
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 1500
Description De‐hulled sterilised seeds were grown in MES culture medium bubbled with air (aerobic-A) at 30°C in the dark for 4 d, coleoptiles were immediately extracted and snap frozen.
Data processing Quality control was confirmed within the Illumina Hiseq software and all reads passing filter were used for downstream analysis.
Filtered reads were mapped onto the O.sativa genome with the International Rice Genome Sequencing Project 1.0 (IRGSP‐1.0) rice genome sequence (from the RAP‐DB) and analysed as previously for MethylC‐seq data (Lister et al., 2011, 2013) and DMRs were identified in the same manner as previously described for this data type (Secco et al., 2015). Briefly, the frequency of cytosine basecalls at reference cytosine positions in the spiked‐in lambda genome was normalized against the total number of base‐calls at reference positions in the lambda genome (which is unmethylated), enabling the calculation of the bisulphite non‐conversion frequency. If regions of differential methylation were within 200 bases of each other and showed the same direction of change in methylation (hypo‐/hyper‐methylation), these were combined into a block and defined as one DMR.
Genome_build: International Rice Genome Sequencing Project 1.0 (IRGSP‐1.0)
Supplementary_files_format_and_content: tab-delimited text files with results of differential methylation analyses (CNN).
Submission date Jun 05, 2018
Last update date Jun 11, 2018
Contact name Reena Narsai
Organization name La trobe University
Street address 5 Ring road
City Bundoora
ZIP/Postal code 3083
Country Australia
Platform ID GPL25149
Series (2)
GSE115372 RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (Methyl-Seq)
GSE115373 RNA-seq and DNA methylomes of germinating rice and developing coleoptiles
BioSample SAMN09371449
SRA SRX4169523

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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