|
| Status |
Public on Jun 04, 2014 |
| Title |
U87 cell line infected with YFP lentivirus |
| Sample type |
RNA |
| |
|
| Source name |
U87 high-grade glioma cell line, YFP lentivirus
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U87
cell type: glioma cell line
lentivirus: YFP
|
| Treatment protocol |
Cells were infected with lentiviruses expressing YFP or YFP-IRES-NICD (activated form of Notch receptor). After 48h, RNA were extracted.
|
| Growth protocol |
U87 high-grade glioma cell line (from ATCC) was grown in 10% serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted with Qiagen RNeasy kits. Quality checks (RIN>8.7) were performed on an Agilent Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
100ng of total RNA was amplified according to the Affymetrix GeneChip® Whole Transcript (WT) Expression assay using the Ambion® WT Expression Kit and Affymetrix labelling kit, which generate sense and labeled DNA.
|
| |
|
| Hybridization protocol |
Targets were prepared with 5.5µg of labelled DNA, and hybrized onto Affymetrix Human Gene ST 1.1 array plates using Affymetrix GeneTitan systems. The GeneTitan performed automatically hybridization, washes, stainings, and scanning of arrays.
|
| Scan protocol |
The arrays were scanned according to Affymetrix recommendations and GeneTitan robotic procedures.
|
| Description |
U87 control
|
| Data processing |
Raw data were controlled using Affymetrix software such as AGCC and Expression Console (www.affymetrix.com). Primary analysis was performed with an external MAQC A sample to validate robustness of data, regarding Affymetrix recommendations and following Institut Curie's genomic platform (Paris, France). Probeset mean, RLE means, AUC were in agreement with Affymetrix recommendations.
|
| |
|
| Submission date |
Feb 21, 2013 |
| Last update date |
Jun 04, 2014 |
| Contact name |
jean-philippe hugnot |
| E-mail(s) |
jean-philippe.hugnot@umontpellier.fr
|
| Organization name |
inserm inm u1191
|
| Lab |
brain plasticity, stem cell and glial tumors
|
| Street address |
IGF INSERM UM 141 rue de la cardonille
|
| City |
MOntpellier |
| State/province |
languedoc |
| ZIP/Postal code |
34094 |
| Country |
France |
| |
|
| Platform ID |
GPL11532 |
| Series (1) |
| GSE44561 |
Effect of Notch1 pathway activation on high-grade glioma cells |
|
