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| Status |
Public on Mar 25, 2021 |
| Title |
6b4 jmj14 |
| Sample type |
SRA |
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| Source name |
Leaf
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Leaf
genotype: 6b4 transgene in jmj14 mutant
developmental stage: 5 weeks
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| Growth protocol |
Plants were grown under short day conditions for five weeks (experiment 1: 6b4-1, 6b4 jmj14, 6b4 jmj14 cmt3 drm2, 6b4 cmt3 drm2) or eight weeks (experiment 2: 6b4-2, 6b4 nac50 nac52, 6b4 ibm1)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from leaf tissue using the Nucleospin Plant II Maxi kit (Macharey Nagel).
Library preparation and sequencing was performed by BGI Genomics (Hong Kong). Briefly, genomic DNA was fragmented to 100-300bp by Sonication, end-repaired and ligated to methylated adaptors. Bisulfite treatment was then performed using the EZ DNA Methylation-Gold kit (Zymo), and the bisulfite-treated fragments were PCR amplified and sequenced as paired-end 100bp reads (PE100) with DNBSEQ technology.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
DNBSEQ-G400 |
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| Data processing |
Pre-processed high quality reads were mapped to the TAIR10 genome using bismark (v0.20.0) with default settings for paired-end libraries (Krueger and Andrews, 2011)
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files with cytosine methylation levels in CG,CHG and CHH contexts.
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| Submission date |
Jun 16, 2020 |
| Last update date |
Mar 25, 2021 |
| Contact name |
Filipe Borges |
| E-mail(s) |
[email protected]
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| Organization name |
Institut Jean-Pierre Bourgin - INRAE
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| Street address |
Route de St-Cyr (RD10)
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| City |
Versailles |
| ZIP/Postal code |
78026 |
| Country |
France |
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| Platform ID |
GPL28290 |
| Series (1) |
| GSE152584 |
Epigenetic differences between transgenes and endogenous genes promote transgene silencing in plants |
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| Relations |
| BioSample |
SAMN15249353 |
| SRA |
SRX8555703 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4618439_6b4_jmj14_CG.wig.gz |
9.0 Mb |
(ftp)(http) |
WIG |
| GSM4618439_6b4_jmj14_CHG.wig.gz |
6.8 Mb |
(ftp)(http) |
WIG |
| GSM4618439_6b4_jmj14_CHH.wig.gz |
19.8 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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