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Status |
Public on Jun 10, 2018 |
Title |
Replicate1_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 |
SAMN09371571 |
SRA |
SRX4169645 |
Supplementary file |
Size |
Download |
File type/resource |
GSM3176827_Replicate1_IP_6mA_peaks.bed.gz |
264.1 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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