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| Status |
Public on Aug 05, 2015 |
| Title |
mouse_placenta |
| Sample type |
SRA |
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| Source name |
placenta
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| Organism |
Mus musculus |
| Characteristics |
tissue: placenta
strain: C57Bl6/J
developmental timepoint: E15.5
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| 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.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| 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.
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| Submission date |
Nov 17, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Janine LaSalle |
| E-mail(s) |
jmlasalle@ucdavis.edu
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| Organization name |
UC Davis
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| Street address |
Medical Microbiology and Immunology
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE63330 |
DNA methylation in mammalian placentas |
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| Relations |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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