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Sample GSM3494248

Query DataSets for GSM3494248

Status

Public on Jan 21, 2019

Title

M1.1

Sample type

SRA

Source name

Adipose from Oregon Health & Science University

Organism

Macaca mulatta

Characteristics

tissue: adipose
Sex: male
age: adult

Treatment protocol

ground in frozen nitrogen with cell crusher

Growth protocol

frozen postmortem samples

Extracted molecule

genomic DNA

Extraction protocol

We homogenized 20 mg of frozen pulverized adipose tissue in nuclei isolation buffer (20 nM Tris-HCl, 50 mM EDTA, 5mM spermidine, 0.15 mM spermine, 0.1% beta meracptoethanol, 40% glycerol, 1% NP40, pH 7.5) with a dounce homogenizer. The homogenate was centrifuged at 1,100 g for 10 minutes at 4C and the pellets resuspended in resuspension buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, pH 7.4).
We ran tagmentation reactions at 37C for 30 minutes, purified samples with Qiagen MinElute kits, and amplified libraries with NEB NextPCR

Library strategy

ATAC-seq

Library source

genomic

Library selection

other

Instrument model

Illumina HiSeq 4000

Description

chromatin accessibile DNA

Data processing

map reads to native genome using bowtie2 default settings for 150 paired end reads
reciprocal liftover to hg19
macs2 for peak calling using paired-end reads algorithm
take union peaks for three species
create dataframe of read counts for each peak, peaks where at least one sample has zero counts are removed
Genome_build: hg19
Supplementary_files_format_and_content: count table

Submission date

Nov 28, 2018

Last update date

Jan 21, 2019

Contact name

Devjanee Swain Lenz

E-mail(s)

ds394@duke.edu

Organization name

Duke University

Street address

130 Bioscience Drive