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Sample GSM3176827 Query DataSets for GSM3176827
Status Public on Jun 10, 2018
Title Replicate1_IP_6mA
Sample type SRA
 
Source name Nipponbare
Organism Oryza sativa Japonica Group
Characteristics tissue: seedling's leaf
cultivar: Nipponbare
age: 12 days
chip antibody: anti-6mA antibody (202-003, Synaptic Systems)
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.
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.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
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;
 
Submission date Jun 05, 2018
Last update date Jun 10, 2018
Contact name chao zhou
E-mail(s) zhouchao@ctgu.edu.cn
Organization name CTGU
Street address No.8,daxuelu Street
City yichang
ZIP/Postal code 443002
Country China
 
Platform ID GPL18525
Series (1)
GSE103145 Identification and analysis of adenine N6-methylation sites in the rice genome
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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