|
| Status |
Public on May 19, 2015 |
| Title |
lung-SARS-CoV-Delta5-REP2 |
| Sample type |
RNA |
| |
|
| Source name |
lung, SARS-CoV-Delta5 infected
|
| Organism |
Mus musculus |
| Characteristics |
infection: SARS-CoV-Delta5
tissue: lung
strain: BALB/c
|
| Treatment protocol |
BALB/c mice were infected at the age of 16 weeks with 100000 pfu and all protocols were approved by the Ethical Review Committee at The Center for Animal Health Research (CISA-INIA). Infected mice were housed in a ventilated rack (Allentown, NJ).
|
| Growth protocol |
8 week-old specific-pathogen-free BALB/c Ola Hsd mice females were purchased from Harlan Laboratories.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At 2 days post infection, lungs from infected mice were collected and homogenized using the gentleMACS Dissociator (Miltenyibiotec). Then, total RNA was extracted using the RNeasy purification kit (Qiagen) according to the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
Preparation of probes and hybridization was performed as described in One-Color Microarray Based Gene Expression Analysis Manual Ver. 6.5, Agilent Technologies. Briefly, for each hybridization 600 ng of Cy3 probes were mixed and added to 5 ul of 10x Blocking Agent, 1 ul of 25x Fragmentation Buffer and Nuclease free water in a 25 μl reaction, incubated at 60ºC for 30 minutes to fragment RNA and stopped with 25 ul of 2x Hybridization Buffer.
|
| |
|
| Hybridization protocol |
The samples were placed on ice and quickly loaded onto arrays, hybridized at 65ºC for 17 hours in a Hybridization oven rotator and then washed in GE wash buffer 1 at room temperature (1 minute) and in GE Wash Buffer 2 at 37ºC (1 minute). Arrays were dried by centrifugation at 2000 rpm for 2 minutes.
|
| Scan protocol |
Images were captured with an Agilent Microarray Scanner and spots quantified using Feature Extraction Software (Agilent Technologies).
|
| Description |
lung, SARS-CoV-Delta5 infected-REP2
|
| Data processing |
Background correction by normexp method (with an offset of 50) and normalization of expression data by adjustment of quantiles were performed using LIMMA package (Smyth, 2004).
|
| |
|
| Submission date |
Jul 08, 2014 |
| Last update date |
May 19, 2015 |
| Contact name |
Juan Carlos Oliveros |
| Organization name |
CNB, CSIC
|
| Street address |
Darwin 3
|
| City |
Cantoblanco |
| State/province |
Madrid |
| ZIP/Postal code |
28049 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13912 |
| Series (1) |
| GSE59185 |
Host responses contributing to the attenuation of severe acute respiratory syndrome coronaviruses missing E protein domains |
|
