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| Status |
Public on Jan 09, 2017 |
| Title |
WT |
| Sample type |
SRA |
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| Source name |
whole seedling
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
tissue: seedling
age: 2 weeks
genotype/variation: wild type
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| Growth protocol |
Plants were grown in plates under long-day conditions (21°C, 16 h light, 8 h dark)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Qiagen Plant DNeasy kit (Qiagen), starting from purified nuclei.
Libraries were constructed starting from 0.5 - 1 μg of genomic DNA, using the NEBNext DNA Sample PrepReagentSet1 (New England Biolabs), following the Illumina Genomic Sample Prep Guide (Illumina).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
wild type
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| Data processing |
For image analysis and base calling, we used the Illumina OLB software version 1.8
The raw reads were trimmed using Trimmomatic (Bolger et al, 2014 Bioinformatics) in order to remove adapter sequences. Reads with an average quality value of at least 15 in a window of 4 nucleotides were trimmed from both ends. After trimming, reads shorter than 16 bases were discarded.
The remaining sequences were aligned against the Arabidopsis thaliana genome TAIR10 version using Bismark (Krueger et al. 2011, Bioinformatics). Duplicated reads were collapsed into one read.
Chloroplast sequences were used to estimate the bisulfite conversion. To account for non-converted DNA, we applied a correction according to (Lister et al. 2013 Science). Briefly, the number of methylated reads were decreased as: m*= max(0, m – nc) (where m* is the corrected number of methylated reads, m is the raw number of methylated reads, n is the total number of reads and c is the conversion rate).
Genome_build: TAIR10
Supplementary_files_format_and_content: For each genotype, the CX_Report generated by Bismark is reported (Krueger et al. 2011, Bioinformatics), after correction for non-converted DNA has been applied.
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| Submission date |
Nov 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Marco Catoni |
| Organization name |
University of Birmingham
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| Department |
School of Biosciences
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| Street address |
Edgbaston
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| City |
Birmingham |
| ZIP/Postal code |
B15 2TT |
| Country |
United Kingdom |
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| Platform ID |
GPL11221 |
| Series (2) |
| GSE89591 |
DNA sequence properties that determine susceptibility to epiallelic switching [Bisulfite-Seq] |
| GSE89592 |
DNA sequence properties that determine susceptibility to epiallelic switching |
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| Relations |
| BioSample |
SAMN05990857 |
| SRA |
SRX2332403 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2384978_wt_processed.txt.gz |
195.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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