|
| Status |
Public on Mar 04, 2014 |
| Title |
9wk: 108 [RRBS] |
| Sample type |
SRA |
| |
|
| Source name |
maternal-High fat_adult-Low fat
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: nine weeks
Sex: Male
maternal diet: High fat
adult diet: Low fat
tissue: liver
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We extracted DNA from the liver of all 9-week-old males using the DNeasy Blood and Tissue kit (Qiagen Inc., Valencia, CA, USA).
Briefly, we digested genomic DNA with MspI before preparing barcoded libraries according to the Illumina protocol. We then size selected DNA molecules of 150-600 bp and bisulfite converted the DNA libraries.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
DS34
|
| Data processing |
We aligned all reads to the mouse genome and determined the methylation status of each CpG for every read covering this position using Bismark
We summarized methylation data using the bismark methylation_extractor and a custom perl script
We summarized data for each CpG using custom scripts in R
Genome_build: mm9
Supplementary_files_format_and_content: SerreRRBSCountsNov2013.txt contains data from all samples. The first and second columns are the chromosome and base location. The following columns are data, with two consecutive columns per sample. The first is the total number of methylated reads at that position, and the second is the total number of reads at that position.
Supplementary_files_format_and_content: SerreRRBSPercentsNov2013.txt contains data from all samples. The first and second columns are the chromosome and base location. The following columns are the percent methylation at each locus for each sample, with one column per sample.
|
| |
|
| Submission date |
Nov 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Matt Cannon |
| E-mail(s) |
matthewvc1@gmail.com
|
| Organization name |
Nationwide Children's Hospital
|
| Department |
Center for Childhood Cancer
|
| Street address |
700 Children's Dr.
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43205 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE52266 |
Maternal Nutrition Induces Pervasive Gene Expression Changes but no Detectable DNA Methylation Differences in the Liver of Adult Offspring [RRBS] |
| GSE52268 |
Maternal Nutrition Induces Pervasive Gene Expression Changes but no Detectable DNA Methylation Differences in the Liver of Adult Offspring |
|
| Relations |
| Reanalyzed by |
GSE120136 |
| BioSample |
SAMN02401287 |
| SRA |
SRX375804 |
