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Sample GSM373869 Query DataSets for GSM373869
Status Public on Feb 25, 2009
Title Cortex 62WT
Sample type RNA
 
Source name cerebral cortex, wild-type
Organism Mus musculus
Characteristics genotype: Cux2+/-
tissue: brain
gender: male
Extracted molecule total RNA
Extraction protocol Cerebral cortex were dissected and total RNA was obtained using Qiagen RNAeasy kit.
Label Cy3
Label protocol For each sample, we have generated cyanine 3-labeled cRNA from one microgram of total RNA, using the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color. Briefly, total RNA is reverse-transcribed using T7-oligo (dT) primer; after first and second strand cDNA synthesis, cRNA is synthesized from the double-stranded cDNA using T7 RNA polymerase, which simultaneously incorporates cyanine 3.
 
Hybridization protocol 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies).
Scan protocol Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays. Images provided by the scanner were analyzed using Feature Extraction software (Agilent Technologies).
Description WT
Data processing Data files from Feature Extraction were imported into GeneSpring® GX software version 9.0. (Agilent Technologies). Quantile normalization was performed and expression values (log2 transformed) were obtained for each probe.
 
Submission date Feb 24, 2009
Last update date Feb 24, 2009
Contact name Ana Dopazo
E-mail(s) adopazo@cnic.es
Phone 34914531217
Organization name CNIC
Department Genomics Unit
Street address Melchor Fdez Almagro
City madrid
ZIP/Postal code 28029
Country Spain
 
Platform ID GPL7202
Series (1)
GSE14971 Comparative gene expression profile of Cux2 knock-out cortex

Data table header descriptions
ID_REF
VALUE Quantile-normalized log2 processed signal

Data table
ID_REF VALUE
GE_BrightCorner 15.1622715
DarkCorner 2.3769462
A_52_P616356 2.695272
A_52_P580582 6.7673383
A_52_P403405 2.8379962
A_52_P819156 5.5042925
A_51_P331831 8.071704
A_51_P430630 2.730668
A_52_P502357 6.0605288
A_52_P299964 4.343085
A_51_P356389 5.5285788
A_52_P684402 9.254068
A_51_P414208 2.7301106
A_51_P280918 11.647954
A_52_P613688 9.733911
A_52_P258194 13.714515
A_52_P229271 5.328307
A_52_P214630 10.757222
A_52_P579519 9.176762
A_52_P979997 2.6955452

Total number of rows: 41252

Table truncated, full table size 907 Kbytes.




Supplementary file Size Download File type/resource
GSM373869.txt.gz 6.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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