|
| Status |
Public on Feb 04, 2015 |
| Title |
MCL001_mock_7hr_2_mRNA |
| Sample type |
RNA |
| |
|
| Source name |
Calu-3 cells, mock treatment (no virus), 7 hours, replicate 2
|
| Organism |
Homo sapiens |
| Characteristics |
time: 7 hours
virus: mock
replicate: 2
|
| Treatment protocol |
Cells were washed twice with PBS and infected with a multiplicity of infection of 5.
|
| Growth protocol |
SCL002.0P: Maintenance, Plating and Virus Infection of Calu-3 cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TCL001.0P: Preparation of Samples from Calu-3 cells for Isolation of RNA.
|
| Label |
Cy3
|
| Label protocol |
Total RNA from each sample was amplified and transcribed into fluorescent cRNA using Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies)
|
| |
|
| Hybridization protocol |
Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.
|
| Scan protocol |
The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).
|
| Data processing |
Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). Quantile normalization and data processing performed using GeneSpring GX v11.5 software (Agilent Technologies).
|
| |
|
| Submission date |
Feb 03, 2015 |
| Last update date |
Aug 31, 2016 |
| Contact name |
Natalie Heller |
| E-mail(s) |
natalie.heller@pnnl.gov
|
| Organization name |
PNNL
|
| Street address |
902 Battelle Blvd.
|
| City |
Richland |
| ZIP/Postal code |
99354 |
| Country |
USA |
| |
|
| Platform ID |
GPL13497 |
| Series (2) |
| GSE65574 |
Human Calu-3 cell transcriptome response to a wild type infectious clone of Middle Eastern Respiratory Syndrome (icMERS) coronavirus and icMERS mutant viruses |
| GSE65575 |
Modeling Host Responses to Understand Severe Human Virus Infections |
|
