|
| Status |
Public on May 23, 2018 |
| Title |
LFD_MeDIP |
| Sample type |
SRA |
| |
|
| Source name |
Epididymal fat macrophages
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Epididymal fat macrophages
gender: Male
strain: C57Bl/6J
age: 22 weeks
weeks of diet: 16 weeks
|
| Treatment protocol |
Epididymal fat stromal vascular fractions (SVF) were isolated by collagenase digestion. F4/80+ cells (ATMs) were purified by labeling SVF cells with anti-F4/80-PE (clone: BM8) followed by immunomagnetic selection with StemCell EasySep PE Positive Selection Kit. Each biological replicate is pools of ATMs isolated from either 60 LFD-fed mice or 30 HFD-fed mice.
|
| Growth protocol |
Mice were fed a 10% low fat diet (Research Diets D12450J) or 60% high fat diet (Research Diets D12492) for 16 weeks starting at 6 weeks of age.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using Qiagen All Prep DNA/RNA/miRNA Universal Kit.
Purified genomic DNA was treated with dsDNA Shearase (Zymo Research, Irvine, CA). DNA fragments sized 200bp to 400 bp were isolated to construct sequencing libraries using Illumina Chip-seq Library Preparation Kit. dsDNA was then denatured and immunoprecipitated with anti 5-methylcytosine antibody using a MeDIP kit from Diagenode (Denville, NJ). Precipitated DNA was purified and sequenced.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
16 weeks of 10% low fat diet
|
| Data processing |
Libraries were sequenced with single-end reads of 75bp. Demultiplexed reads were filtered for full length reads. Filtered reads were mapped to the mouse genome build mm9 using Bowtie software allowing 2 mismatches in the read. Mapped reads were filtered to uniquely mapped reads then analyzed with MEDIPS software.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data are provided as .WIG files that can be viewed in a genome browser to observe methylation signal of genomic regions.
|
| |
|
| Submission date |
May 22, 2018 |
| Last update date |
May 24, 2018 |
| Contact name |
Prakash Nagarkatti |
| E-mail(s) |
prakash@mailbox.sc.edu
|
| Organization name |
University of South Carolina School of Medicine
|
| Street address |
6439 Garners Ferry Road
|
| City |
Columbia |
| State/province |
SC |
| ZIP/Postal code |
29209 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE114792 |
DNA methylation-mediated regulation of adipose tissue macrophages during high-fat diet-induced obesity |
|
| Relations |
| BioSample |
SAMN09238662 |
| SRA |
SRX4116209 |
