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Sample GSM373868 Query DataSets for GSM373868
Status Public on Feb 25, 2009
Title Cortex 15WT
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 65┬║C 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 15.140269
DarkCorner 2.5261216
A_52_P616356 3.124184
A_52_P580582 6.69573
A_52_P403405 3.1421354
A_52_P819156 5.6680927
A_51_P331831 7.852883
A_51_P430630 3.15711
A_52_P502357 4.874417
A_52_P299964 4.1257005
A_51_P356389 5.7231364
A_52_P684402 9.1714945
A_51_P414208 3.1530066
A_51_P280918 11.544786
A_52_P613688 10.1793995
A_52_P258194 13.608163
A_52_P229271 5.3156867
A_52_P214630 10.344291
A_52_P579519 9.407303
A_52_P979997 3.1077173

Total number of rows: 41252

Table truncated, full table size 907 Kbytes.




Supplementary file Size Download File type/resource
GSM373868.txt.gz 6.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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