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Sample GSM2083773 Query DataSets for GSM2083773
Status Public on Apr 06, 2017
Title 48h Macrophage LPS Rep 2 ATAC-seq
Sample type SRA
 
Source name Macrophage
Organism Homo sapiens
Characteristics induction: PMA+LPS
time: 48 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)
[bed]
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).
[bigWig]
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
E-mail(s) ricardnr@uci.edu
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
Relations
BioSample SAMN04543271
SRA SRX1621380

Supplementary file Size Download File type/resource
GSM2083773_48h-MacLPS-Rep2.bw 102.6 Mb (ftp)(http) BW
GSM2083773_48h-MacLPS-Rep2.peaks.bed.gz 644.9 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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