|
| Status |
Public on Nov 28, 2019 |
| Title |
CD64_ID8_4w_b4_1 |
| Sample type |
RNA |
| |
|
| Source name |
CD64_ID8_4w
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Intra-peritoneal tumor
cell type: macrophage
phenotype: CD64+CCR2+
time (in weeks): 4
strain: C57Bl/6
treatment: ID8
|
| Treatment protocol |
To evaluate the impact of the tumor-microenvironment on PM phenotype, we performed global gene expression analysis using microarrays on bulk PM from naïve mice and at different time points (4, 6 or 8 weeks) during ID8 tumor progression.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Each cell subset was purified by flow cytometry and total RNA was extracted with the Qiagen RNeasy Plus Micro Kit, according to the manufacturer protocol. The lineage cocktail used was a combination of antibodies against CD19 (B cells), T cell receptor beta chain (alpha/beta T cells and NK T cells), NK1.1 (NK and NK T cells) and Ly6G (neutrophiles).
|
| Label |
biotin
|
| Label protocol |
20 ng of RNA from each sample was used to synthesize biotinylated probes, according to a double amplification protocol using MessageAmpTM II aRNA Amplification Kit (Ambion).
|
| |
|
| Hybridization protocol |
Following fragmentation and end-labeling, 2 μg of cDNAs were hybridized for 16 hours at 45°C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.
|
| Data processing |
The data were RMA normalized in R and Bioconductor, using the oligo package.
|
| |
|
| Submission date |
Feb 11, 2019 |
| Last update date |
Nov 28, 2019 |
| Contact name |
Thien-Phong Vu Manh |
| Organization name |
CIML
|
| Street address |
163 avenue de Luminy
|
| City |
marseille |
| ZIP/Postal code |
13288 |
| Country |
France |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE126378 |
Tumor-induced cholesterol efflux from macrophages drives IL-4 mediated reprogramming and tumor progression |
|
