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Sample GSM1037117 Query DataSets for GSM1037117
Status Public on Mar 31, 2013
Title Lung-X31-12h-S3
Sample type RNA
 
Source name wild-type C57BL/6J mice lung tissue
Organism Mus musculus
Characteristics strain: C57BL/6J
infection (influenza strain): X31
time (hours): 12
Treatment protocol Virus aliquots stored at -80C; quick thaw to RT and immediate dilution. Viruses diluted to 1x10^5 PFU/30ul (3.33x10^6 PFU/ml) in ice-cold 1x PBS in polystyrene tubes. Virus dilution maintained at 4C until use. Mice are all female C57BL/6J from Jackson Lab.
Extracted molecule total RNA
Extraction protocol Mice were sacrificed by CO2 inhalation. Whole lungs (right side) removed and homogenized (with bead homogenizer) in 1 ml Trizol. Samples snap frozen in liquid nitrogen.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using Agilent’s Low Input Quick Amp One-Color Labeling Kit according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and
 
Hybridization protocol 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using the Agilent G3-1-color scan setting for 8x60k arrays.
Description Lung tissue after stimulation with either PR8, VN, X31 or Mock for 12 hours
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20101029).
 
Submission date Nov 14, 2012
Last update date Mar 31, 2013
Contact name Aderem Lab
E-mail(s) alan.diercks@seattlechildrens.org
Organization name Seattle Children's Research Institute
Lab Aderem Lab
Street address 307 Westlake Avenue North, Suite 500
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL10787
Series (1)
GSE42285 Host response in the lung to influenza infection with PR8, VN or X31 strains at 12, 16 and 24 hours

Data table header descriptions
ID_REF
VALUE Quantile Normalized Data using Analyst (GeneData, Basel, Switzerland)

Data table
ID_REF VALUE
A_55_P2051983 3.209641
A_52_P169082 18.73063
A_30_P01028193 3.2257402
A_52_P237997 14.141546
A_51_P414243 2408.5195
A_55_P2136348 4.5264707
A_51_P108228 18.105915
A_30_P01033363 15.864442
A_55_P2049737 8.748123
A_30_P01024440 508.70648
A_30_P01025554 5356.499
A_30_P01031558 51.917774
A_30_P01030675 3.3051033
A_51_P328014 2356.5735
A_30_P01019108 219.23561
A_55_P2056220 2971.5112
A_55_P1985764 20379.797
A_52_P108321 303.4901
A_55_P2018002 194.57683
A_52_P123354 1254.3103

Total number of rows: 55681

Table truncated, full table size 1285 Kbytes.




Supplementary file Size Download File type/resource
GSM1037117_Lung-X31-12h-S3.txt.gz 12.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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