|
| Status |
Public on Jun 07, 2011 |
| Title |
Donor 2, Culture Cells at ALI-D21 |
| Sample type |
RNA |
| |
|
| Source name |
Human nasal epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: human nasal mucosa
differentiation step: Terminal mucociliary differentiation
rin number: 9
amount in (µg): 0.3
|
| Treatment protocol |
At confluency (day 7 after seeding), cultures cells were switched in air-liquid interface (ALI) in the differentiating medium.
|
| Growth protocol |
Dissociated cells from nasal polyps were either seed on collagen-type IV coated permeable supports for differentiation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNAs was performed according to the manufacturer's instructions and purified on a Qiagen RNeasy kit column (Qiagen, France) according to the manufacturer’s instructions. Purity and concentration of total RNA samples were first evaluated using Nanodrop spectrophotometer (Nanodrop, Labtech, Palaiseau, France). Ratio 260/280 and 260/230 were checked to be near a value of 2. Then, RNA samples were ran in a RNA nano-chip into a 2100 Bioanalyzer System (Agilent Tecnologies, France) to verify the integrity or degradation of the RNA samples.
|
| Label |
Biotin-Affy
|
| Label protocol |
Total RNAs were labelled and hybridized using the whole Transcript (WT) Sense Target Labeling and Control Reagents, fluidics and scanning instrumentation and basic analysis software, as indicated by the manufacturer’s instructions. Slides were quantified using Feature Extraction software (Agilent Technologies).
|
| |
|
| Hybridization protocol |
Affymetrix protocol for huGene chips.
|
| Scan protocol |
GeneChip scanner 3000 7G, GeneChip Operating Software v1.4
|
| Description |
Gene expression data
|
| Data processing |
The data were processed using the RMA (Robust Multi-Chip Average) algorithm, which performs a background correction, a normalization step, and a probe-level summary (Irizarry et al., 2003). Data were normalized following a linear model and an empirical Bayes method in R (Bioconductor) using LIMMA package.
|
| |
|
| Submission date |
Jun 04, 2010 |
| Last update date |
Jun 07, 2011 |
| Contact name |
Kevin Lebrigand |
| Organization name |
IPMC/CNRS
|
| Lab |
Functional Genomics Platform of Nice-Sophia-Antipolis, France.
|
| Street address |
660 route des lucioles
|
| City |
Valbonne - Sophia-Antipolis |
| ZIP/Postal code |
06560 |
| Country |
France |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE22142 |
Transcriptome analysis during the time course of regeneration of the human airway mucociliary epithelium |
| GSE22147 |
microRNAs-449 control vertebrate multi-ciliogenesis by repressing Notch signalling |
|
