|
| Status |
Public on Dec 22, 2008 |
| Title |
WT 6 hr A |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
A549, WT infection, 6 hr
|
| Organism |
Homo sapiens |
| Characteristics |
A549 human respiratory epithelial cell line from lung carcinoma derived from 58 year old Caucasian male
|
| Treatment protocol |
Sucrose purified wild-type, C(F170S), and P(C-) HPIV1 in Opti-MEM supplemented with 1.2 % Trypsin was inoculated at a multiplicity of infection of 5. 300 pg/mL (60 IU/mL) IFN-beta in Opti-MEM was used to treat A549 cells.
|
| Growth protocol |
A549 cells were grown in F12 (Ham) media supplemented with 5% fetal bovine seruma, 4 mM L-glutamine, 0.1 mg/mL gentamicin. Cells were subcultured 1:3, twice a week
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cellular homogenization, lysis, and RNA extraction was prepared using the QIAshredder and Qiagen RNeasy mini kits as per the manufacturer's protocols (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
Sample labeling with Cy5 and Cy3 from 1 µg total RNA was performed using the Agilent 2-Color Low RNA Input Linear Amp Kit PLUS (Agilent Technologies) as per the manufacturer's protocols (Agilent).
|
| |
|
| Channel 2 |
| Source name |
A549, Mock Infection, 6 hr
|
| Organism |
Homo sapiens |
| Characteristics |
A549 human respiratory epithelial cell line from lung carcinoma derived from 58 year old Caucasian male
|
| Treatment protocol |
Sucrose purified wild-type, C(F170S), and P(C-) HPIV1 in Opti-MEM supplemented with 1.2 % Trypsin was inoculated at a multiplicity of infection of 5. 300 pg/mL (60 IU/mL) IFN-beta in Opti-MEM was used to treat A549 cells.
|
| Growth protocol |
A549 cells were grown in F12 (Ham) media supplemented with 5% fetal bovine seruma, 4 mM L-glutamine, 0.1 mg/mL gentamicin. Cells were subcultured 1:3, twice a week
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cellular homogenization, lysis, and RNA extraction was prepared using the QIAshredder and Qiagen RNeasy mini kits as per the manufacturer's protocols (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Sample labeling with Cy5 and Cy3 from 1 µg total RNA was performed using the Agilent 2-Color Low RNA Input Linear Amp Kit PLUS (Agilent Technologies) as per the manufacturer's protocols (Agilent).
|
| |
|
| |
| Hybridization protocol |
Samples were hybridized at 10 RPM at 65 °C for 18 hours as per the two-color microarray-based gene expression analysis version 5.5 protocol (Agilent Technologies).
|
| Scan protocol |
Microarrays were scanned with an Agilent Microarray Scanner (Part Number G2565BA). Agilent Feature Extraction Software 9.5.1 was used for image acquisition. The single pass scan resolution was 5 micrometers, and extended dynamic range was activated.
|
| Description |
Replicate A
|
| Data processing |
Normalized values were derived from: 1) Averaging on-chip replicates; 2) Cy5/Cy3; 3) per chip normalization to the median
|
| |
|
| Submission date |
Sep 04, 2008 |
| Last update date |
Dec 22, 2008 |
| Contact name |
Jim Boonyaratanakornkit |
| E-mail(s) |
jim.boonyaratanakornkit@gmail.com
|
| Phone |
301-594-2589
|
| Organization name |
NIH - NIAID
|
| Department |
LID
|
| Lab |
RVS
|
| Street address |
50 South Dr, Bldg 50, Rm 6513
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE12664 |
Analysis of wild-type and C mutant human HPIV1 and interferon beta treatment in human respiratory epithelial A549 cells |
|
