|
| Status |
Public on Oct 15, 2016 |
| Title |
CM-C treatment at 3 hours, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
P388D1 cell line exposed to CM-C after 3 hours
|
| Organism |
Mus musculus |
| Characteristics |
cell line: P388D1
cell type: macrophage-like cell line
cell type: methylcholanthrene induced
treated with: control-conditioned medium from non-infected macrophages (CM-C)
treatment duration: 3hrs
|
| Treatment protocol |
Non-infected macrophages were treated with conditioned medium from macrophages persistently infected with RSV virus (CM-MΦP) or with control-conditioned medium from non-infected macrophages (CM-C) for 3 and 12 h at 37ºC, 5% CO2
|
| Growth protocol |
Cell culturer were maintained in RPMI 1640 cell-culture medium (GIBCO/BRL, Grand Island, NY, USA), supplemented with 5% fetal bovine serum, 1% penicillin-streptomycin and 1 μM 2-mercaptoethanol at 37 °C and 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed using the AxyPrep Multisource Total RNA Miniprep kit (Axygen Scientific, Union City, CA, USA), according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the Affymetrix Whole-Transcript Sense Target Labeling Protocol
|
| |
|
| Hybridization protocol |
Labeled DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array in a hybridization cocktail . Washing and staining steps were carried out using GeneChip Fluidics Station 450
|
| Scan protocol |
GeneChip® Scanner 3000 7G (Affymetrix, Santa Clara CA)
|
| Description |
CM-C3h_2
Gene expression data from P388D1 cell line exposed to CM-C after 3 hours
|
| Data processing |
Raw intensity data were pre-processed and quantile normalized using the robust multi-array average (RMA) expression measure function implemented within the oligo package of bioconductor. Log2 transformed expression values, obtained after RMA, were used to analyze the differential expressions between different groups was analyzed using empirical Bayes method implemented in the LIMMA package and P values were computed.
|
| |
|
| Submission date |
Oct 14, 2016 |
| Last update date |
Oct 15, 2016 |
| Contact name |
Ivan Salido-Guadarrama |
| E-mail(s) |
silvervann@gmail.com
|
| Phone |
52(55) 54871700
|
| Organization name |
Instituto Nacional de Enfermedades Respiratorias
|
| Lab |
Computational Biology
|
| Street address |
Calz. de Tlalpan 4502
|
| City |
Mexico City |
| ZIP/Postal code |
14080 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL16570 |
| Series (1) |
| GSE88743 |
Expression data from non-infected macrophages treated with conditioned medium from macrophages persistently infected with RSV virus |
|
