|
| Status |
Public on Aug 27, 2018 |
| Title |
MBD_OIL_39-8 |
| Sample type |
SRA |
| |
|
| Source name |
epididymal fat
|
| Organism |
Mus musculus |
| Characteristics |
Sex: male
strain: CD-1
exposure: vehicle
tissue: epididymal fat
|
| Treatment protocol |
Pregnant CD-1 mice were exposed to BPA (500 ug/kg/day) or vehicle (corn oil) orally during gestational day 9-18. Pups were fed ad libitum with a standard chow (Purina 5001, 4% fat) and grown until 19 weeks after birth.
|
| Growth protocol |
CD-1 mice were subjected to timed mating.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Epididymal fat was collected from 19-weeks-old males by dissection and subjected to isolation of genomic DNA and total RNA using AllPrep Mini kit (QIAGEN).
Genomic DNA was fragmented to 200-300 bp in length by sonication and subjected to enrichment of methylated DNA fragments using biotinylated, recombinant human methylCpG binding domain 2 (MBD2) protein provided in Invitrogen MethylMiner kit.
Total RNA was subjected to ribosomal RNA removal using RiboMinus Eukaryote System v2 kit (Life Technologies).
DNA fragments enriched for CpG methylation was subjected to deep sequencing library construction using the SOLiD fragment library core kit (Thermo Fisher) and the EZ Bead emulsion PCR system (Life Technologies).
Ribosomal RNA-depleted total RNA was subjected to deep sequencing library construction using the SOLiD Total RNA-seq kit (Thermo Fisher) and the EZ Bead emulsion PCR system (Life Technologies).
|
| |
|
| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
AB 5500 Genetic Analyzer |
| |
|
| Description |
MBD_OIL_4
DNA for CpG methylome analysis
|
| Data processing |
SOLiD 5500 deep sequencer run (single, 50 nt) was performed with single index to generate color-space data in XSQ format.
XSQ files were subjected to analyses using LifeScope software package (Life Technologies), which provided RNA-seq and MBD-seq (as MethylMiner-seq) modules. LifeScope aligned color space read data to ther NCBI37/mm9 mouse genome reference sequence to generate BAM files.
LifeScope processed RNA-seq BAM files to generate normalized amounts of mRNA expression based no the mm9 annotation.
MBD-seq BAM files generated by LifeScope were subjected to analysis using the MEDIPS package of R/bioconductor to generate annotated peaks of DNA methylation. MEDIPS performs normalization using the edgeR package of R/bioconductor.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Microsoft Excel xlsx spreadsheets including normalized relative intensity of mRNA expression and DNA methylation.
|
| |
|
| Submission date |
Nov 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Toshi Shioda |
| E-mail(s) |
tshioda@partners.org
|
| Phone |
(617) 726-3425
|
| Organization name |
MGH Cancer Center
|
| Department |
Center for Cancer Research
|
| Lab |
Molecular Profiling Lab
|
| Street address |
Building 149 - 7th Floor, 13th Street
|
| City |
Charlestown |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL16790 |
| Series (1) |
| GSE107198 |
DNA methylomes and RNA transcriptomes in 19-weeks-old CD-1 male epididymal white adipose tissues with or without prenatal exposure to 500 ug/kg/day Bisphenol A |
|
| Relations |
| BioSample |
SAMN08048982 |
| SRA |
SRX3412379 |
