|
| Status |
Public on Jun 01, 2011 |
| Title |
16HBE_uninfected_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
16HBE cells incubated without A. fumigatus conidiospores
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: human bronchial epithelial cell line 16HBE
infection: control
|
| Treatment protocol |
Confluent 16HBE monolayers were incubated with A. fumigatus conidiospores at a ratio of 10 conidiospores per cell (Infected), or without condiospores (Control), for 6 hours at 37°C in DMEM supplemented with FBS, antibiotics, sodium pyruvate, and sodium bicarbonate.
|
| Growth protocol |
16HBE cells were maintained at 37°C in DMEM supplemented with FBS, antibiotics, sodium pyruvate, and sodium bicarbonate. Cells were passaged at confluence.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Following incubation, cells were lysed in 450μl buffer RLT (Qiagen, Hilden, Germany), and RNA was extracted using the RNeasy Mini Kit with QIAshredder (Qiagen), following the manufacturer’s recommendations. RNA yield from each sample was determined using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE).
|
| Label |
Cy3
|
| Label protocol |
Cy3-labeled complementary RNA (cRNA) was generated following Agilent’s Low RNA Input Linear Amplification Protocol, and its quantity and specific activity assessed using a NanoDrop ND-1000 (Thermo Scientific).
|
| |
|
| Hybridization protocol |
Labeled cRNA (1.65μg) was fragmented for 30 minutes, hybridized to microarrays for 17 hours at 65°C in the Agilent hybridization oven, and washed with Agilent wash buffers, according to the manufacturer's protocols.
|
| Scan protocol |
Arrays were scanned using the Agilent DNA Microarray Scanner at a resolution of 5μm and Agilent’s Feature Extraction software version 9.1 was used for quantification of signal intensities and to produce a quality control report for each microarray, using the default protocol for a one-colour array.
|
| Description |
Gene expression in 16HBE incubated for 6 hours in the absence of A. fumigatus conidiospores
|
| Data processing |
Raw signals were first normalized by flooring all values smaller than 1 to 1, then dividing each value by the median intensity value of the array.
|
| |
|
| Submission date |
Jun 15, 2009 |
| Last update date |
Jun 01, 2011 |
| Contact name |
Scott Tebbutt |
| E-mail(s) |
scott.tebbutt@hli.ubc.ca
|
| Organization name |
UBC - iCAPTURE Centre
|
| Street address |
St. Paul's Hospital - Rm 166 - 1081 Burrard St.
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6Z 1Y6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6480 |
| Series (2) |
| GSE16628 |
Functional genomics of human bronchial epithelial cells interacting with conidiospores of Aspergillus fumigatus |
| GSE16637 |
Transcriptomic analysis of interactions between Aspergillus fumigatus conidiospores and human bronchial epithelial cells |
|
