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Status |
Public on Jan 21, 2019 |
Title |
M1.1 |
Sample type |
SRA |
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Source name |
Adipose from Oregon Health & Science University
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Organism |
Macaca mulatta |
Characteristics |
tissue: adipose Sex: male age: adult
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Treatment protocol |
ground in frozen nitrogen with cell crusher
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Growth protocol |
frozen postmortem samples
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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
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 4000 |
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Description |
chromatin accessibile DNA
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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
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Submission date |
Nov 28, 2018 |
Last update date |
Jan 21, 2019 |
Contact name |
Devjanee Swain Lenz |
E-mail(s) |
ds394@duke.edu
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Organization name |
Duke University
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Street address |
130 Bioscience Drive
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City |
Durham |
State/province |
NC |
ZIP/Postal code |
27708 |
Country |
USA |
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Platform ID |
GPL23949 |
Series (1) |
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Relations |
BioSample |
SAMN10492192 |
SRA |
SRX5073716 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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