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Sample GSM1462881 Query DataSets for GSM1462881
Status Public on Aug 01, 2014
Title P14 (MBD-Seq) replicate2
Sample type SRA
 
Source name Cardiac left ventricle - neonatal day 14
Organism Mus musculus
Characteristics gender: Male
age: P14
tissue: cardiac left ventricle
strain: C57BL/6
Treatment protocol N/A
Growth protocol Experimental Animals and Tissue Collection: All protocols were approved by The University of Queensland Animal Ethics Committee. Male C57BL/6 mice (The Jackson Laboratory, ME) were used for genome-wide DNA methylation and mRNA expression profiling during post-natal development (P1 and P14). For DNA and RNA analysis, atrial tissues were removed from ventricles (septum intact) and ventricles were blotted and weighed before snap-freezing in liquid nitrogen for storage at -80C.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA for DNA methylation profiling was isolated using the DNeasy Blood & Tissue Kit (Qiagen). DNA was fragmented by BioRuptor sonication (Diagenode, Denville, NJ). Fragmented DNA was analyzed with bioanalyzer, and 1microgram of sonicated DNA underwent methyl-CpG enrichment using the MethylMiner™ Methylated DNA Enrichment Kit (Invitrogen).
Library preparation was undertaken using 5 ng of methyl-enriched DNA using the NEBNext DNA Library Preparation Kit for Illumina (New England Biolabs). Library DNA was quantified with MultiNA capillary electrophoresis instrument with DNA-500 kit. Libraries were sequenced at a concentration of 10 pM on Genome Analyzer IIx instrument for 36 cycles. Illumina base-calling was performed off-line with OLB v1.8.
 
Library strategy MBD-Seq
Library source genomic
Library selection MBD2 protein methyl-CpG binding domain
Instrument model Illumina Genome Analyzer IIx
 
Data processing Basecalling with Illumina pipeline software (OLB v1.8)
Fastx quality trimmer was used to remove low quality bases from the 3' end of the read (base quality <30)
The mouse genome was downloaded from the Ensembl ftp site (version GRCm38.70/mm10). Reads were aligned to the mouse genome with BWA (aln algorithm v0.6) with default settings. GRCm38.70
Datasets from each developmental stage were pooled and peak identification was performed using MACS peak caller with default settings. Annotation of differentially methylated regions (DMRs) with Ensembl genes was performed with BedTools intersect command. Reads aligned to DMRs with a strict mapping quality (Q≥20) were counted with BedTools and used to construct a data matrix consisting of regions with an average of 10 reads or more per sample across the experiment. Statistical significance of these regions was ascertained using edgeR (v3.2.4) with the independent replicate data.
Genome_build: GRCm38.70/mm10
Supplementary_files_format_and_content: Count matrix
 
Submission date Jul 31, 2014
Last update date May 15, 2019
Contact name Mark D Ziemann
E-mail(s) mark.ziemann@gmail.com
Organization name Deakin University
Department Life and Environmental Sciences
Street address 75 Pigdons rd
City Waurn Ponds
State/province VIC
ZIP/Postal code 3216
Country Australia
 
Platform ID GPL11002
Series (2)
GSE59969 Genome-wide DNA methylation analysis reveals dynamic changes in the cardiac methylome during post-natal heart development (MBD-Seq)
GSE59971 Genome-wide DNA methylation analysis reveals dynamic changes in the cardiac methylome during post-natal heart development
Relations
BioSample SAMN02948102
SRA SRX667352

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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