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Sample GSM2572243 Query DataSets for GSM2572243
Status Public on Jan 02, 2019
Title cortex oxBS-seq rep2
Sample type SRA
 
Source name cortex
Organism Mus musculus
Characteristics strain: C57BL/6
age: 8 week
tissue: cortex
Extracted molecule genomic DNA
Extraction protocol The tissues for the technical replicates are from independent mouse, and at least two replicates are included in different assay as indicated. Genomic DNA (Qiagen, Cat#: 51306) were extracted according to the manufacturers’ instructions.
The sequencing libraries were constructed as described with little modifications. Briefly, genomic DNA (0.5 to 1 μg) was end-repaired, A-tailed, and ligated to methylated adaptors following the manufacturer’s instructions. The ligated fragments were then purified using Bio-Rad Micro Bio-Spin P-6 SSC column (SSC buffer). After the purification, the samples were denaturized using 1M NaOH and oxidized using oxidant solution (15mM KRuO4 in 0.05M NaOH). After the purification, the DNA was further directed to bisulfite conversion using the EZ DNA methylation Gold kit (Zymo Research) according to the instruction manual. The library was sequenced using Illumina HiSeq X Ten. Paired reads were mapped uniquely to the reference genome (mm10, UCSC) by Bismark. Efficient conversion of 5hmC to uracil were calculated by spiked 5hmC control from Zymo Research (Cat#: D5405)
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model HiSeq X Ten
 
Description oxBS-seq
Data processing Paired reads were mapped uniquely to the reference genome (mm10, UCSC) by Bismark.The 5mC level of the biological replicates were calculated in 1Mb regions throughout the genome
After PCR duplication remove, we calculated the 5hmC or 5mC level of each CpG sites. The processed bigwig files indicate the 5hmC and 5mC level in CpG sites coverd by more than 5 reads.
genome build: mm10
processed data files format and content: bigwig or text files with 5hmC or 5mC level or gene FPKM. 5hmC or 5mC level calculation is as follows: we counted the number of 'C' bases from sequencing reads as hydroxymethylated or methylated (denoted as NC) and the number of 'T' bases as unmodified (denoted as NT). The hydroxymethylation level or methylation level was estimated as NC/(NC + NT) in 1Mb windows. Bigwig files are available on the series record.
 
Submission date Apr 10, 2017
Last update date May 15, 2019
Contact name Qin Ma
E-mail(s) qinma@big.ac.cn
Organization name Beijing Institute of Genomics
Department Chinese Academy of Sciences
Street address NO.1 Beichen West Road, Chaoyang District
City Beijing
ZIP/Postal code 100101
Country China
 
Platform ID GPL21273
Series (1)
GSE97568 Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the mouse brain
Relations
BioSample SAMN06704545
SRA SRX2731662

Supplementary file Size Download File type/resource
GSM2572243_cortex_3_5mc_1M.txt.gz 329.1 Kb (ftp)(http) TXT
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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