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Sample GSM1190993 Query DataSets for GSM1190993
Status Public on Jul 22, 2014
Title NHP1_Anhui01_Trachea_d3_1
Sample type RNA
 
Source name Animal NHP1, Anhui01 infection, trachea, day3
Organism Macaca fascicularis
Characteristics tissue: trachea
infection: Anhui01
time point: d3
animal id: NHP1
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

Data table header descriptions
ID_REF
VALUE Log2 quantile-normalized signal intensity

Data table
ID_REF VALUE
A_01_P1691476 3.348893565
A_01_P1785371 2.662274255
A_01_P1674786 3.473477948
A_01_P1827606 2.686109009
A_01_P1715436 2.566617423
A_01_P1705531 2.51155616
A_01_P1803076 3.423437747
A_01_P006014 3.462216097
A_01_P1733141 3.65489248
A_01_P1712451 3.325610934
A_01_P1688441 3.050928659
A_01_P1788126 2.918462144
A_01_P1686151 2.350688523
A_01_P1789596 2.974547437
A_01_P005831 3.553125113
A_01_P004004 2.671814947
A_01_P1745001 2.724942644
A_01_P011483 3.067074156
A_01_P1746631 3.065466511
A_01_P1789806 3.423478304

Total number of rows: 43603

Table truncated, full table size 1091 Kbytes.




Supplementary file Size Download File type/resource
GSM1190993_US93503719_254853410011_S01_GE1_107_Sep09_1_4.txt.gz 11.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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