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Sample GSM1545829 Query DataSets for GSM1545829
Status Public on Aug 05, 2015
Title mouse_placenta
Sample type SRA
Source name placenta
Organism Mus musculus
Characteristics tissue: placenta
strain: C57Bl6/J
developmental timepoint: E15.5
Extracted molecule genomic DNA
Extraction protocol DNA was purified using Qiagen's Puregene kit. MethylC-seq libraries were made by sonicating the genomic DNA to ~300 bp and ligating methylated Illumina adapters to the ends. The library was bisulfite converted, amplified for 14 cycles, and sequenced.
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
Data processing genome version: mm10
Reads were mapped to the respective genomes using BS Seeker.
100 bp reads were trimmed at the 3' end to 85 bp for BS Seeker alignment. BS Seeker parameters: -e 85 -m 3 -a adapter2
Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage. Methylation data for both DNA strands were combined. Onle one read starting at a given gneomic coordinate was kept to eliminate clonal replicates. Red=80-100% methylation, green=60-80%, blue=1-60%, black=0%.
Supplementary_files_format_and_content: BED file with the name fields giving the % methylation at that CpG site.
Submission date Nov 17, 2014
Last update date May 15, 2019
Contact name Janine LaSalle
Organization name UC Davis
Street address Medical Microbiology and Immunology
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
Platform ID GPL13112
Series (1)
GSE63330 DNA methylation in mammalian placentas
BioSample SAMN03196683
SRA SRX760451

Supplementary file Size Download File type/resource
GSM1545829_mouse_placenta_methylation.tar.gz 111.0 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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