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Sample GSM535967 Query DataSets for GSM535967
Status Public on Oct 05, 2010
Title m_Blood_MBD_M
Sample type SRA
 
Source name Blood
Organism Mus musculus
Characteristics tissue: Blood
age: 30 weeks
chip antibody/mbd affinity column: MBD Affinity Purifcation (MAP)-seq (recombinant human MBD domain)
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using phenol/chloroform and sheared to approximately 400 bp using sonication. Methylated DNA was purified by two step MBD Affinity Purification as described in Skene et al., 2010.
Libraries were prepared as follows using enzymes from New England Biolabs (NEB). End Repair was carried out by incubating immunoprecipitated DNA with T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase for 30 minutes at 20 C. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP for 30 minutes at 37 C to yield a protruding 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Ligated DNA was extracted using MiniElute PCR clean up columns (Qiagen) and PCR amplified with Illumina primers for 10-12 cycles. Library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated by gel extraction. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Sequencing was performed at the Wellcome Trust Sanger Institute; Hinxton, Cambridge, UK.
 
Library strategy MBD-Seq
Library source genomic
Library selection MBD2 protein methyl-CpG binding domain
Instrument model Illumina Genome Analyzer
 
Description MBD affinity chromatography
Data processing Alignment: Single-end sequence reads were mapped to the mouse genome (NCBIm37) using MAQ (http://maq.sourceforge.net/). Reads with a mapping score greater or equal to 30 where retained. Alignment was performed at the Wellcome Trust Sanger Institute; Hinxton, Cambridge, UK.
 
Submission date Apr 21, 2010
Last update date May 15, 2019
Contact name Adrian P Bird
E-mail(s) A.Bird@ed.ac.uk
Phone 0131 6508695
Fax 0131 6505379
Organization name The University of Edinburgh
Department WTCCB
Lab Bird Lab
Street address Mayfield Road
City Edinburgh
State/province Midlothian
ZIP/Postal code EH9 3JR
Country United Kingdom
 
Platform ID GPL9185
Series (1)
GSE21442 Comprehensive analysis of orphan CpG islands identifes novel promoters with conserved DNA methylation dynamics
Relations
SRA SRX019603
BioSample SAMN00011935

Supplementary file Size Download File type/resource
GSM535967_concat_2608_3.bedgraph.gz 25.1 Mb (ftp)(http) BEDGRAPH
GSM535967_concat_2608_5.bedgraph.gz 18.7 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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