|
| Status |
Public on Nov 17, 2022 |
| Title |
M1, biological rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
M1
|
| Organism |
Mus musculus |
| Characteristics |
strain: Balb/c
genotype: WT
Sex: female
cell type: M1 macrophage
treatment: Control
|
| Treatment protocol |
Next, the cells were incubated with 100 ng/mL of lipopolysaccharide and 20 ng/mL of recombinant mouse IFN-γ (R&D Systems, Minneapolis, MN, USA), for 24–48 h to achieve M1 polarization.
|
| Growth protocol |
Bone marrow cells were isolated from tibias and femurs of Balb/c mice and cultured in DMEM supplemented with 10 ng/mL of colony-stimulating factor-1 (CSF-1; Gibco, Carlsbad, CA, USA) and 10% FBS for 7 d. The culture medium was changed every other day.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs for miRNA profiling were isolated using the miRNeasy® Mini Kit. RNA purity and integrity were evaluated by ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA), Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).
|
| Label |
FlashTag Biotin HSR RNA label
|
| Label protocol |
poly*(A) tailing and ligation were done using FlashTag Biotin HSR RNA labelling kit
|
| |
|
| Hybridization protocol |
Hybridization was done using GeneChip hybridization oven, followed by washing and staining using Genechip fluidics station.The labeled RNA was heated to 99°C for 5 minutes and then to 45°C for 5 minutes. RNA-array hybridization was performed with agitation at 60 rotations per minute for 16 hours at 48°C on an Affymetrix® 450 Fluidics Station. The chips were washed and stained using a Genechip Fluidics Station 450 (Affymetrix, Santa Clara, California, United States).
|
| Scan protocol |
The chips were then scanned with an Affymetrix GCS 3000 canner (Affymetrix, Santa Clara, California, United States).
|
| Description |
miR expression in M1 macrophages
|
| Data processing |
Signal values were computed using the Affymetrix® GeneChip™ Command Console software. Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC). The CEL files import, miRNA level RMA+DABG-All analysis and result export using Affymetrix® Expression Console™ Software. Array data were filtered by probes annotated species. The comparative analysis between test sample and control sample was carried out using fold-change. For a significant DEmiRNA set, Hierarchical cluster analysis was performed using complete linkage and Euclidean distance as a measure of similarity. All Statistical test and visualization of differentially expressed genes was conducted using R statistical language v. 3.1.2
The CEL files import, miRNA level RMA+DABG-All analysis and result export using Affymetrix® Expression Console™ Software. Array data were filtered by probes annotated species.The comparative analysis between test sample and control sample was carried out using fold-change. For a significant DEmiRNA set, Hierarchical cluster analysis was performed using complete linkage and Euclidean distance as a measure of similarity. All Statistical test and visualization of differentially expressed genes was conducted using R statistical language v. 3.1.2.
|
| |
|
| Submission date |
Nov 17, 2022 |
| Last update date |
Nov 17, 2022 |
| Contact name |
Byungheon Lee |
| E-mail(s) |
leebh@knu.ac.kr
|
| Phone |
+82-10-5501-3457
|
| Organization name |
Kyungpook National University
|
| Department |
School of Medicine
|
| Lab |
Department of Biochemistry and Cell Biology
|
| Street address |
680 Guckchaebosang-ro, Jung-gu
|
| City |
Daegu |
| State/province |
Outside U.S. & Canada |
| ZIP/Postal code |
41944 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL19117 |
| Series (1) |
| GSE218160 |
miR expression microarray analysis on M2 macrophages treated with epigenetic modifiers |
|
