|
| Status |
Public on Apr 06, 2017 |
| Title |
168h Monocyte-derived Mac PMA LPS-Rep2 RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Monocyte-derived Macrophage
|
| Organism |
Homo sapiens |
| Characteristics |
induction: PMA+LPS
time: 168 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 |
total RNA |
| Extraction protocol |
Approximately ~1-2 million HL-60 and differentiated cells were collected for RNA-seq. Briefly, cells were assessed for cell viability, counted and washed with PBS. RNA-seq was performed as previously described (Mortazavi et al., 2008).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
RNA-seq reads were mapped to the hg38 reference genome using STAR (Dobin et al., 2013) aligner.
Reads were mapped to Gencode version 20 gene annotations using Cufflinks (Trapnell et al., 2010).
FPKM values were normalized for batch effects using Combat (Johnson et al., 2007).
Genome_build: hg38
|
| |
|
| Submission date |
Mar 09, 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) |
| GSE79044 |
Dynamic gene regulatory networks of human myeloid differentiation [RNA-seq] |
| GSE79046 |
Dynamic gene regulatory networks of human myeloid differentiation |
|
| Relations |
| BioSample |
SAMN04543638 |
| SRA |
SRX1621812 |
