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Sample GSM1191009 Query DataSets for GSM1191009
Status Public on Jul 22, 2014
Title NHP4_Anhui01_Trachea_d3_4
Sample type RNA
 
Source name Animal NHP4, Anhui01 infection, trachea, day3
Organism Macaca fascicularis
Characteristics tissue: trachea
infection: Anhui01
time point: d3
animal id: NHP4
developmental stage: adult
biological replicate: 4
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 Replicate4
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 3.413092647
A_01_P1785371 3.01192519
A_01_P1674786 3.421627437
A_01_P1827606 2.966538794
A_01_P1715436 2.615688397
A_01_P1705531 2.502374441
A_01_P1803076 3.249436679
A_01_P006014 3.326675302
A_01_P1733141 3.609359038
A_01_P1712451 3.26309537
A_01_P1688441 2.803887479
A_01_P1788126 2.687015304
A_01_P1686151 2.291850644
A_01_P1789596 3.037602525
A_01_P005831 3.379022201
A_01_P004004 2.507884719
A_01_P1745001 2.831228041
A_01_P011483 3.167034723
A_01_P1746631 3.043260956
A_01_P1789806 3.476903008

Total number of rows: 43603

Table truncated, full table size 1091 Kbytes.




Supplementary file Size Download File type/resource
GSM1191009_US93503719_254853410024_S01_GE1_107_Sep09_1_1.txt.gz 11.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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