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| Status |
Public on Jun 10, 2018 |
| Title |
Replicate2_IP_6mA |
| Sample type |
SRA |
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| Source name |
Nipponbare
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| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: seedling's leaf
cultivar: Nipponbare
age: 12 days
chip antibody: anti-6mA antibody (202-003, Synaptic Systems)
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| Growth protocol |
Seedling were grown in one-half-strength Murashige and Skoog medium under a 16-h-light/8-h-dark cycle at 30°C for 12 days.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For 6mA IP-seq, the total genomic DNA was extracted from 12 days of leaves using the DNeasy plant mini kit (Qiagen) with overnight RNase A treatment.
Briefly, 5g genomic DNA extracted from 12 days leaf was sonicated into 200 ~ 400bp and end-repaired, followed by adapter ligation. DNA was denatured at 95 degree for 10 min, and chilled on ice for 10 min. A part of denatured DNA was saved as input. The remaining of DNA was immunoprecipitated with anti-6mA antibody (202-003, Synaptic Systems) overnight at 4 degrees. DNA was eluted by 6mA salt competition. After DNA fragment’s size selection and PCR amplification, the DNA fragments were sequenced with the NextSeq 500.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Library strategy: 6mA IP-Seq
Quality Control: fastqc
Remove low quality data: 6mA-IP-seq raw data's low quality reads were removed from raw data by Trimmomatic.
6mA-IP-seq clean reads were aligned to the rice MSU7.0 reference genome by bowtie
6mA-IP-seq's peaks calling were used with MACS software with default parameters.
6mA_modification.gff was analyzed using the SMRT analysis platform for DNA 6mA modification detection which identifies 6mA-modified bases based on inter-pulse duration ratios in the sequencing data
Genome_build: MSU7.0 rice reference genome;rice MH63 reference genome
Supplementary_files_format_and_content: bed files were generated using MACS software;
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| Submission date |
Jun 05, 2018 |
| Last update date |
Jun 10, 2018 |
| Contact name |
chao zhou |
| E-mail(s) |
zhouchao@ctgu.edu.cn
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| Organization name |
CTGU
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| Street address |
No.8,daxuelu Street
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| City |
yichang |
| ZIP/Postal code |
443002 |
| Country |
China |
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| Platform ID |
GPL18525 |
| Series (1) |
| GSE103145 |
Identification and analysis of adenine N6-methylation sites in the rice genome |
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| Relations |
| BioSample |
SAMN09371569 |
| SRA |
SRX4169647 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3176829_Replicate2_IP_6mA_peaks.bed.gz |
253.9 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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