|
| Status |
Public on Apr 06, 2017 |
| Title |
120h Macrophage LPS Rep 3 ATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
Macrophage
|
| Organism |
Homo sapiens |
| Characteristics |
induction: PMA+LPS
time: 120 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 |
SAMN04543276 |
| SRA |
SRX1621390 |
