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Sample GSM830249 Query DataSets for GSM830249
Status Public on Feb 15, 2012
Title Cast_MethylC_Seq
Sample type SRA
Source name Frontal cortex
Organism Mus musculus
Characteristics strain: Cast/EiJ
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 Five µg of genomic DNA was extracted from the frontal cortex of the F1 crosses and was spiked in with 25 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented by sonication to 100-600 bp. Purified DNA fragments were end-repaired and ligated to paired-end cytosine- methylated adapters provided by Illumina. Size-selected adapter-ligated DNA was treated with sodium bisulfite using the EZ DNA methylation-Gold Kit (Zymo Research). The resulting DNA molecules were enriched by PCR, purified and sequenced following standard protocols from Illumina. The average insert sizes of the paired-end libraries are 140bp and 143bp, with the standard deviation of 47bp and 49bp, for the F1i and F1r strains, respectively.
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
Data processing MethylC-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. PCR duplicates for each library were removed with the Picard program(Picard 2011).
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 GPL13112
Series (2)
GSE30199 Base-resolution analyses of parent-of-origin and sequence dependent allele specific DNA methylation in the mouse genome (ChIP-seq and Methyl-seq)
GSE33722 Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation
Reanalyzed by GSE77019
SRA SRX108103
BioSample SAMN00760531

Supplementary file Size Download File type/resource
GSM830249_Cast_MethylC_Seq_crick.bam 13.9 Gb (ftp)(http) BAM
GSM830249_Cast_MethylC_Seq_watson.bam 14.0 Gb (ftp)(http) BAM
GSM830249_Cast_mC_crick.txt.gz 1.8 Gb (ftp)(http) TXT
GSM830249_Cast_mC_watson.txt.gz 1.8 Gb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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