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Sample GSM3543733 Query DataSets for GSM3543733
Status Public on Jan 07, 2019
Title T17 (RRBS)
Sample type SRA
 
Source name white adipose tissue
Organism Macaca mulatta
Characteristics condition: testosterone
Sex: female
age: 4 years old
tissue: white adipose tissue
Treatment protocol Visceral (omental) adipose tissue biopsies were collected in year 3 of treatment.
Growth protocol Young adult female rhesus macaques received testosterone (to mimic hyperandrogenemia) or control cholesterol implants for 3 years. Animals were maintained either on monkey chow (control) or high-fat western-style diet.
Extracted molecule genomic DNA
Extraction protocol DNA extracted using the AllPrep DNA/RNA purification kit (QIAGEN) according to the manufacturer’s instructions
RRBS libraries were generated starting with genomic DNA extracted from WAT. Overnight digestion was performed on ~200ng DNA using the restriction enzyme MspI (New England Biolabs, Ipswich, MA). Reaction clean-up was performed with AMPure XP magnetic beads (Beckman Coulter, Brea, CA) before use with the NEXTflex Bisulfite-Seq Kit (Bioo Scientific Corporation, Austin, TX) for library preparation. The digested DNA was quantified and then ~80ng was end-repaired, A-tailed, and ligated with the NEBNext Methylated Adaptor (New England Biolabs). The ligated DNA was cleaned and then size-selected using AMPure XP magnetic beads to produce a final library size of 350 bp. Bisulfite conversion was performed with the EZ DNA Methylation-Gold Kit (Zymo Research, Irvine, CA) before carrying out PCR amplification with NEBNext Multiplex Oligos for Illumina (New England Biolabs) to barcode each library. Two AMPure XP bead cleans were performed and the resulting libraries were quantified with the Qubit High Sensitivity dsDNA Assay (Life Technologies, Eugene, OR) and the Bioanalyzer High Sensitivity DNA Kit (Agilent, Santa Clara, CA).
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina NextSeq 500
 
Description ECP7.RRBS.processed.methRates.txt
Data processing base calling
Sequencing reads were evaluated with FastQC (v0.11.5)
adapters and low quality bases trimmed with TrimGalore (v0.4.2) with parameter --rrbs
trimmed reads aligned to Mmul8 reference genome with Bismark (v0.16.1) using default parameters
acquire methylated and unmethylated counts per CpG as "cytosine report" file using bismark_methylation_extractor function
calculate methylation rate per CpG as number of methylated counts divided by total counts
DMC analysis: limited to CpGs with at least 10X coverage in at least 4 of the 6 replicates among all 4 groups (841,143 CpGs)
arcsin transform methylation rate values and use Limma to fit 4 group model and perform pariwise contrasts
DMR analysis: use same CpGs and pvalues obtained from limma DMC analysis as input into comb-p software to find DMRs
Genome_build: Mmul8
Supplementary_files_format_and_content: tab delimited text file of a filtered methylation rate table containing the methylation rate (methylated count / coverage) for CpGs used in DMC and DMR analysis
Supplementary_files_format_and_content: the first column "CpG_ID" contains the chr_start coordinates for the CpG using ensembl's Mmul8 reference genome and 1-based start coordinates. There is then a column for each sample.
 
Submission date Jan 06, 2019
Last update date Jan 08, 2019
Contact name Brett Davis
E-mail(s) davibr@ohsu.edu
Organization name Oregon Health and Science University
Street address 3181 SW Sam Jackson Park Rd
City Portland
State/province Oregon
ZIP/Postal code 97239
Country USA
 
Platform ID GPL21120
Series (2)
GSE124708 Hyperandrogenemia and western-style diet act synergistically on transcription and DNA methylation in visceral adipose tissue of a non-human primate model [RRBS]
GSE124709 Hyperandrogenemia and western-style diet act synergistically on transcription and DNA methylation in visceral adipose tissue of a non-human primate model
Relations
BioSample SAMN10697993
SRA SRX5210323

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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