|
| Status |
Public on Aug 01, 2014 |
| Title |
P1 (MBD-Seq) replicate3 |
| Sample type |
SRA |
| |
|
| Source name |
Cardiac left ventricle - neonatal day 1
|
| Organism |
Mus musculus |
| Characteristics |
gender: Male
age: P1
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 |
Burnet Institute
|
| Department |
Bioinformatics Working Group
|
| Street address |
85 Commercial Rd
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3004 |
| 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 |
SAMN02948130 |
| SRA |
SRX667350 |
