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| Status |
Public on Dec 31, 2018 |
| Title |
wildtype col-0 |
| Sample type |
SRA |
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| Source name |
whole seedling
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| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: 12-d-old
tissue: whole seedling
genotype: wild type
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| Growth protocol |
Twelve-d-old seedlings grown at 22 oC, 16/8 hr of light time, 70% of relative humidity
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from whole seedlings and sent to Macrogen (http://www.macrogen.com/eng/) for bisulfite treatment, library preparation and sequencing.
Bisulfite treatment and following library construction were performed using standard Illumina protocols.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Low quality trimming and artificial sequence trimming was performed with trim_galore (version 0.2.8) with parameters "--paired -t -a TACAGTCCGACGATC"
BS-seq data mapping was performed with bwa-meth (version 0.09).
The 5mC ratio calling was performed with bwa-meth (version 0.09) and Bis-SNP (version 0.82.2) with parameters "--map-q 60 -T BisulfiteGenotyper -C CG,1 -C CHG,1 -C CHH,1 -out_modes EMIT_ALL_CYTOSINES"
Biased bases at ends of mapped reads were surveyed and trimmed (--trim 3,3)
Genome_build: TAIR10
Supplementary_files_format_and_content: a tab-delimited text file contains; cytosine locus, 5mC/non-5mC reads counts and sequence context
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| Submission date |
Dec 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jin Hoe Huh |
| E-mail(s) |
huhjh@snu.ac.kr
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| Organization name |
Seoul National University
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| Department |
Dept Plant Science
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| Street address |
Gwanak-gu
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| City |
Seoul |
| ZIP/Postal code |
151-921 |
| Country |
South Korea |
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| Platform ID |
GPL13222 |
| Series (1) |
| GSE64569 |
BS-seq of ros1-3, ros1-4 with wildtype col-0 |
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| Relations |
| BioSample |
SAMN03273967 |
| SRA |
SRX825526 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1574493_wt.5mC.txt.gz |
193.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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