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| Status |
Public on Aug 23, 2017 |
| Title |
fie_4D_seedling_5mC |
| Sample type |
SRA |
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| Source name |
4 day old seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
background strain: Col0
genotype: fie
developmental stage: 4 day old seedlings
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| Growth protocol |
Seeds of Arabidopsis thaliana accession Columbia-0 grown in soil under long day conditions (16h light/8h dark) at 23°C were hand-dissected to extract the embryo. Mutants of fie at the mature embryonic stage were identified by their enhanced dormancy; genotyping verified homozygousity for the T-DNA insertion. Wild type Col0 and fie seedlings were grown on 1/2 MS media plates and harvested at the earliest stage allowing distinctinction between wild type and mutant (4 days after germination).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extraction was performed using standard CTAB/Phe-Chloroform purification. Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturers instructions and its quality was validated using RNA 6000 NanoChip (Agilent).
1 ug of total DNA was shipped to BGI-genomics, Shenzen, China where samples where further treated for quality control, bisulfite conversion, library preparation and squencing. 1ug of total RNA was sent to Fasteris SA, Plan-les-Ouates, Switzerland, performing sRNA extracting, library production and sequencing.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
bisulfite converted gDNA
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| Data processing |
Bisulfite-Seq reads were mapped to reference genomes (TAIR 10) using the Bowtie2 alignment algorithm allowing one mismatch and only uniquely mapped reads were used for further analysis
Bisulfite-Seq Analysis methylated regions (MRs) were defined by tiling the genome into 100 base pair bins and comparing the number of called Cs and Ts with the reference genome. Bins with absolute methylation difference of 0.4, 0.2, 0.1 for CG, CHG, CHH, respectively, and Benjamini-Hochberg corrected FDR < 0.01 (Fisher’s exact test) were selected. To avoid 100 bp bins with few cytosines, we selected for bins with at least 4 cytosines that are each covered by at least 10 reads in each sample.MRs within 100 bp of each other were merged.
sRNA of 21-22nt and 24nt reads were selected before mapping against the reference genomes (Release 10) using the Bowtie alignment algorithm allowing one mismatch
Genome_build: Arabidopsis thaliana (TAIR10)
Supplementary_files_format_and_content: bedGraph = Chromosome, START- and STOP-position, level of methylation for MRs; gff with normalized density for small RNA-seq
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| Submission date |
Aug 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Bouyer |
| E-mail(s) |
[email protected]
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| Organization name |
CNRS
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| Department |
ENS-Lyon/RDP
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| Lab |
EpiCDev
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| Street address |
46 Allée d'Italie
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| City |
Lyon |
| ZIP/Postal code |
69364 |
| Country |
France |
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| Platform ID |
GPL13222 |
| Series (1) |
| GSE85975 |
DNA methylation dynamics during early plant life |
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| Relations |
| BioSample |
SAMN05609438 |
| SRA |
SRX2040720 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2290020_fie-4d-seedlings_CG.bedgraph.gz |
543.8 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM2290020_fie-4d-seedlings_CHG.bedgraph.gz |
218.9 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM2290020_fie-4d-seedlings_CHH.bedgraph.gz |
202.7 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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