|
| Status |
Public on Oct 27, 2015 |
| Title |
BAL Cells control biological rep5_NC |
| Sample type |
RNA |
| |
|
| Source name |
Control
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Bronchial alveolar lavage cells
group: NC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).
Total RNA was extracted from BALF cells the suspended in Trizol solution using the QIACube system (Qiagen, Valencia, CA). RNA quality was determined using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), and only samples with an RIN higher than 7 used for microarray experiments.
|
| Label |
Cy3-CTP
|
| Label protocol |
Cy3-CTP labeled RNA was prepared according to the standard Agilent protocol from 50ng total RNA. Labeled RNA was hybridized to Agilent Human GE 4 × 44 Kv2 whole human genome microarrays.
|
| |
|
| Hybridization protocol |
RNA was hybridized to Agilent Human GE 4 × 44 Kv2 whole human genome microarrays
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4X44K array slides
|
| Description |
Bronchial alveolar lavage cells
|
| Data processing |
The data was extracted using the Agilent Feature Extraction software 10.7.3.1 (Agilent Technologies)
The data set was normalized by cyclic-LOESS with use of Bioconductor package as described previously (Wu W et. al. 2005). Probes which did not map to an Entrez ID were excluded
|
| |
|
| Submission date |
Apr 15, 2015 |
| Last update date |
Oct 27, 2015 |
| Contact name |
Jadranka Milosevic |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Pittsburgh
|
| Street address |
2330 Tilbury Avenue
|
| City |
Pittsburgh |
| State/province |
PA - Pennsylvania |
| ZIP/Postal code |
15217 |
| Country |
USA |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
|
