|
| Status |
Public on Jul 22, 2014 |
| Title |
NHP5_Anhui01_LL3_d6_1 |
| Sample type |
RNA |
| |
|
| Source name |
Animal NHP5, Anhui01 infection, lung lesion, day6
|
| Organism |
Macaca fascicularis |
| Characteristics |
tissue: lung lesion
infection: Anhui01
time point: d6
animal id: NHP5
developmental stage: adult
biological replicate: 1
|
| Treatment protocol |
Tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNAlater. After a 4ºC incubation for overnight, samples were stored at -80ºC prior to further processing. Tissues were removed from RNAlater, washed in a small volume of RLT buffer, homogenized in 10-20 volumes (w/v) RLT with an equal volume of 70% ethanol and stored at -80°C until RNA isolation.
|
| Growth protocol |
8 adult cynomolgus macaques (Macaca fascicularis) were infected under anesthesia with 7x10^6 TCID50 A/H7N9/Anhui01/2013 by combined oral, intraocular, intranasal, and intratracheal instillation. Four animals each were humanely sacrificed on days 3 and 6 for necropsy and collection of lung, lung lesion, and trachea samples.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All lysates were processed simultaneously. Samples were thawed and two additional volumes of RLT buffer with 0.01 volumes of 2-mercaptoethanol were added, followed by an additional two volumes of 70% ethanol. RNA was then extracted using QIAGEN microRNeasy spin columns per the manufacturer's protocol. Low-yield samples were concentrated using the RNA Clean and Concentrator (Zymo Research).
|
| Label |
Cy3
|
| Label protocol |
The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.
|
| |
|
| Hybridization protocol |
The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 8X60K rhesus macaque (Design ID 048534) array.
|
| Scan protocol |
Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.
|
| Description |
Replicate1
|
| Data processing |
Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were normalized using the quantile normalization method available in GeneData Analyst 7.6.
|
| |
|
| Submission date |
Jul 17, 2013 |
| Last update date |
Jul 22, 2014 |
| Contact name |
Michael Katze |
| E-mail(s) |
data@viromics.washington.edu
|
| Organization name |
University of Washington
|
| Department |
Microbiology
|
| Lab |
Michael G. Katze, Ph.D
|
| Street address |
Rosen Building 960 Republican St.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-4325 |
| Country |
USA |
| |
|
| Platform ID |
GPL17465 |
| Series (1) |
| GSE48976 |
Cynomolgus macaque model of H7N9 influenza infection |
|
