|
| Status |
Public on Jan 13, 2017 |
| Title |
BEECH_cleanair_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
A549, beech clean air
|
| Organism |
Homo sapiens |
| Characteristics |
organ: lung
cell line: A549
tissue: epithelium
|
| Treatment protocol |
Confluent layers of A549 cells were exposed to the diluted log wood and pellet combustion aerosols for 4 h. At the same time clean air exposures of confluent layers of A549 cells were performed as reference under the same conditions.
|
| Growth protocol |
Human lung epithelial cell line A549 (ATCC® CCL-185™) was cultured in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum (FBS), 100 U/ml penicillin, 100 mg/ml streptomycin (all from Life Technologies, Darmstadt).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Rneasy Mini plus Kit (Qiagen) including genomic DNA removal according to the manufacturer s protocol.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
Purified labeled cRNA was fragmented and hybridized on Human Gene Expression Microarrays (Sure Print G3 Human Gene Expression Microarray 8x60 K, Agilent, Waldbronn, Germany) using ozone-barrier slide covers and hybridization gasket slides (Ozone-Barrier Slide Cover Kit, Hybridization Gasket Slide Kit and Gene Expression Hybridisation Kit, Agilent, Waldbronn, Germany) for 17h at 65°C in a hybridization oven.
|
| Scan protocol |
After washing (Gene Expression Wash Buffer Kit, Agilent, Waldbronn, Germany) slides were scanned (Agilent C microarray scanner, Agilent, Waldbronn, Germany).
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 028004_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Jan 12, 2017 |
| Last update date |
Jan 13, 2017 |
| Contact name |
Sebastian Oeder |
| E-mail(s) |
sebastian.oeder@lrz.tum.de
|
| Organization name |
Technische Universität München
|
| Department |
Center for Allergy and Environment (ZAUM)
|
| Street address |
Biedersteinerstr. 29
|
| City |
Munich |
| ZIP/Postal code |
80802 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13607 |
| Series (1) |
| GSE93557 |
Lung cell responses to wood combustion aerosols |
|
