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Sample GSM2083759 Query DataSets for GSM2083759
Status Public on Apr 06, 2017
Title 3h Macrophage Rep 3 ATAC-seq
Sample type SRA
Source name Macrophage
Organism Homo sapiens
Characteristics induction: PMA
time: 3 hr
Treatment protocol Differentiation of HL-60 cells into macrophage (Murao et al., 1983), monocytes (Mangelsdorf et al., 1984) and neutrophils (Breitman et al., 1980) was performed as previously described. Additionally, monocytes (120 hours post-differentiation) were stimulated with PMA to induce differentiation into monocyte-derived macrophages. LPS stimulation at 48, 120, and 168 hours for specific cell-types was induced at a final concentration of 100ng/ml for ~3h, immediately followed by expression analysis.
Growth protocol HL-60 cells (ATCC) were grown in Modified Dulbecco's Medium in a final concentration of 20% FBS with penicillin antibiotics (1%). Cells were routinely cultured at a density of 1x10^6 cells/ml.
Extracted molecule genomic DNA
Extraction protocol Approximately 50,000 HL-60 and differentiated cells were collected for ATAC-seq. ATAC-seq was performed as previously described (Buenrostro et al., 2013) with one amendment. DNA size exclusion was utilized after library generation to enrich for accessible chromatin ranging from 100-400bp.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Data processing Library strategy: ATAC-seq
ATAC-seq reads were mapped to the hg38 reference genome using bowtie (Langmead et al., 2009). Using parameters (bowtie -S --trim3 7 --chunkmbs 3000 -p 32 -m 3 -v 2 --best --strata -X 3000)
HOMER was used to call ATAC-seq peaks. Using parameters (findPeaks Mapp.dir -size 500 -minDist 50 -fdr 0.01) and findPeaks Mapp.dir -minDist 50 -fdr 0.01 -style factor). ‘Narrow’ and ‘broad’ regions were then merged into a single bed file for each replicate.
Counts were normalized for batch effects using Combat (Johnson et al., 2007).
BAM was generated from SAM file using samtools/0.1.18
BedTools genomeCoverageBed was used to convert BAM to bedGraph with hg38 chromosome sizes.
bedGraphToBigWig from UCSC was used to generate bigWig files.
Genome_build: hg38
Supplementary_files_format_and_content: bed, bigWig
Submission date Mar 08, 2016
Last update date May 15, 2019
Contact name Ricardo Noel Ramirez
Organization name University of California Irvine
Department Developmental and Cell Biology
Street address 2300 Biological Sciences III
City Irvine
State/province California
ZIP/Postal code 92697
Country USA
Platform ID GPL18573
Series (2)
GSE79019 Dynamic gene regulatory networks of human myeloid differentiation [ATAC-seq]
GSE79046 Dynamic gene regulatory networks of human myeloid differentiation
BioSample SAMN04543253
SRA SRX1621366

Supplementary file Size Download File type/resource 208.8 Mb (ftp)(http) BW
GSM2083759_3h-Mac-Rep3.peaks.bed.gz 402.7 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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