|
| Status |
Public on Jun 14, 2018 |
| Title |
MG_CO_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Mammary gland tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
gender: female
tissue: Mammary gland tissue
|
| Treatment protocol |
Males were fed etiher a control or low-protein (LP) diet from 3 to 10 weeks of age. Mature sperm was collected from fathers and Mammary tissue from their female offspring.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from paternal sperm and offspring’s mammary tissue (n=3/group). Methylated DNA was eluted by the MethylMiner Methylated DNA Enrichment Kit (Invitrogen). Briefly, one microgram of genomic DNA was sheared by sonication and captured by MBD proteins. The methylated DNA was eluted and used to generate Methyl-CpG binding domain-based capture (MDBCap) libraries
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to custom miRNA reference sequence derived from mm10 whole genome using bismark v0.18.1_dev and bowtie2 v2.3.4.1 with parameters -q --parallel 2 -N 1 --score-min L,0,-0.2 --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Coverage results and beta value were calculted from R package GenomicAlignment and GenomicFeatures.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include abundance and beta value for each sample
|
| |
|
| Submission date |
May 14, 2018 |
| Last update date |
Jun 14, 2018 |
| Contact name |
Lu Jin |
| E-mail(s) |
lj74@georgetown.edu
|
| Organization name |
Georgetown University
|
| Department |
Oncology
|
| Lab |
NRB Room W405B
|
| Street address |
3970 Reservoir Rd NW
|
| City |
Washington |
| State/province |
D.C. |
| ZIP/Postal code |
20057 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE114422 |
Paternal malnutrition programs offspring’s breast cancer risk and tumor metabolism in a mouse model (MBD-seq) |
| GSE114423 |
Paternal malnutrition programs offspring’s breast cancer risk and tumor metabolism in a mouse model |
|
| Relations |
| BioSample |
SAMN09206628 |
| SRA |
SRX4081203 |
