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Sample GSM830150 Query DataSets for GSM830150
Status Public on Feb 15, 2012
Title F1i_FspEI_Seq
Sample type SRA
Source name Frontal cortex
Organism Mus musculus
Characteristics strain: 129X1/SvJ x Cast/EiJ
gender: male
tissue: frontal cortex
Growth protocol The crosses of the two mouse strains 129x1/SvJ (129) and Cast/EiJ (Cast) were performed at Jackson Laboratories ( and the male mice F1 offspring and males of each of the two parental strains were shipped to investigator laboratories at 8 to 9 weeks of age.
Extracted molecule genomic DNA
Extraction protocol A total of 500ng genomic DNA isolated from IMR90, MEF, and the frontal cortex of F1i and F1r was digested in parallel by the DNA methylation dependent restriction enzyme FspEI. FspEI recognizes the CmC site (the second cytosine is methylated and can be in the context of CG, CHG or CHH) and creates a 5’ protruding end 17 bases downstream of the methylcytosine. A similar experiment was performed by incubating the F1i genomic DNA with a DNA methylation independent restriction enzyme BstNI. The digested DNA was gel purified, size selected for fragments within 100-600bp. The resulting DNA was then prepared as genomic DNA libraries for high-throughput sequencing (Illumina).
Library strategy MRE-Seq
Library source genomic
Library selection Restriction Digest
Instrument model Illumina Genome Analyzer II
Data processing FspEI-Seq reads were mapped using Novoalign (Novocraft, Malaysia) with adapter sequences stripped. Novoalign permits gapped alignment by allowing more than two mismatches per read (up to 8 for high quality base calls on single end reads and 16 on paired-end reads) that particularly benefits sequencing read mapping around SNPs and indels. Only reads that were perfectly mapped were used to determine the positions of methylcytosines on the same strand.
Submission date Nov 09, 2011
Last update date May 15, 2019
Contact name Wei Xie
Organization name UCSD
Street address 9500 Gilman Dr. CMM East, Room 2071
City San Diego
ZIP/Postal code 92093
Country USA
Platform ID GPL9250
Series (2)
GSE33579 Base-resolution analyses of parent-of-origin and sequence dependent allele specific DNA methylation in the mouse genome (MRE-seq)
GSE33722 Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation
SRA SRX107371
BioSample SAMN00760460

Supplementary file Size Download File type/resource
GSM830150_F1i.FspEI.129.bam 90.7 Mb (ftp)(http) BAM
GSM830150_F1i.FspEI.129.crick.mC.txt.gz 710.7 Kb (ftp)(http) TXT
GSM830150_F1i.FspEI.129.watson.mC.txt.gz 712.6 Kb (ftp)(http) TXT
GSM830150_F1i.FspEI.Cast.bam 88.7 Mb (ftp)(http) BAM
GSM830150_F1i.FspEI.Cast.crick.mC.txt.gz 645.8 Kb (ftp)(http) TXT
GSM830150_F1i.FspEI.Cast.watson.mC.txt.gz 643.6 Kb (ftp)(http) TXT
GSM830150_F1i.FspEI.bam 762.8 Mb (ftp)(http) BAM
GSM830150_F1i.FspEI.crick.mC.txt.gz 4.7 Mb (ftp)(http) TXT
GSM830150_F1i.FspEI.unassigned.bam 608.6 Mb (ftp)(http) BAM
GSM830150_F1i.FspEI.watson.mC.txt.gz 4.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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