|
Status |
Public on Apr 06, 2017 |
Title |
12h Neutrophil Rep 3 ATAC-seq |
Sample type |
SRA |
|
|
Source name |
Neutrophil
|
Organism |
Homo sapiens |
Characteristics |
induction: DMSO/ATRA time: 12 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.
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|
|
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
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|
|
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 |
SAMN04543285 |
SRA |
SRX1621399 |