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Sample GSM337893 Query DataSets for GSM337893
Status Public on Aug 21, 2009
Title Foxa3-/-_Saline_rep1
Sample type RNA
 
Source name Lung tissue from Foxa3 KO challenged with saline
Organism Mus musculus
Characteristics C57BL/6
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Qiagen RNEasy columns. RNA integrity was confirmed using an Agilent 2100 Bioanalyzer
Label Cy3
Label protocol 400ng of RNA was amplified and labeled using the One-Color Agilent Low RNA Input Linear Amplification Kit
 
Hybridization protocol Labeled cRNA was assessed using the Nandrop ND-100 , and equal amounts of Cy3 labeled target were hybridized to Agilent whole genome custom arrays (platform acc# GPL7202). Hybridizations were performed for 14 hrs, according to the manufacturers protocol.
Scan protocol Arrays were scanned using the Agilent microarray scanner
Description 11 arrays were hybridized and represent 3 lung samples for groups WT saline, WT OVA and KO OVA. There are 2 samples for the KO saline group.
Data processing Raw signal intensities were extracted with Feature Extraction v9.1 software (Agilent). The dataset was normalized using the quantile normalization method. The median feature pixel intensity was used as the raw signal before normalization and no background subtraction was performed.
 
Submission date Oct 28, 2008
Last update date Aug 21, 2009
Contact name Andrea J Barczak
Organization name UCSF Sandler Center Functional Genomics Core Facility
Street address 1550 4th St Rock Hall 545
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platform ID GPL7202
Series (1)
GSE13382 Distinct roles of FOXA2 and FOXA3 in allergic airway disease

Data table header descriptions
ID_REF
VALUE Normalized log2 signal intensity

Data table
ID_REF VALUE
A_52_P616356 6
A_52_P580582 11.02974212
A_52_P403405 6.39699391
A_52_P819156 7.008173931
A_51_P331831 11.30914042
A_51_P430630 6.287922211
A_52_P502357 5.821339151
A_52_P299964 6.700439718
A_51_P356389 7.16216242
A_52_P684402 9.239869707
A_51_P414208 6.164449871
A_51_P280918 9.32474311
A_52_P613688 8.898807482
A_52_P258194 6.650399036
A_52_P229271 6.540568381
A_52_P214630 6.550396999
A_52_P579519 8.145005782
A_52_P979997 5.810863708
A_52_P453864 6.619386331
A_52_P655842 6.619386331

Total number of rows: 41174

Table truncated, full table size 995 Kbytes.




Supplementary file Size Download File type/resource
GSM337893.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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