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Sample GSM668596 Query DataSets for GSM668596
Status Public on May 13, 2011
Title Wild-type control 3
Sample type RNA
 
Source name WT_3
Organism Mus musculus
Characteristics genotype: Wild-type
tissue: brain amygdala
genetic background: C57BL/6
Growth protocol Experiments were performed on three-month old wild-type (C57BL/6) or neuropsin-/- mice backcrossed to C57BL/6 for 12 generations. Animals were housed three to five per cage in a colony room with a 12 hour light/dark cycle (lights on at 7AM) with ad libitum access to commercial chow and tap water. The experiments were approved by the UK Home Office and the UoL Ethical Committee.
Extracted molecule total RNA
Extraction protocol Amygdalae tissue have been submerged in RNAlater solution (Qiagen) and stored at -20°C until RNA purification. Total RNA was extracted using RNeasy Lipid Tissue Mini Kit (Qiagen) as per manufacturer's instructions. The rybosomal fraction of RNA was significantly reduced with RiboMinus Kit (Invitrogen) and the RNA integrity has been verified by electrophoresis using Agilent Bioanalyser 2100.
Label biotin
Label protocol 1 ug of total RNA was processed using a ribosomal RNA reduction step (RiboMinus Kit, Invitrogen) and labeled according to the Whole Transcriptome Sense Kit (Affymetrix).
 
Hybridization protocol Hybridization protocol 10 ug of fragmented cRNA was hybridized to each array for 17 hours at 45°C with rotation at 60rpm according to the Affymetrix standard protocol.
Scan protocol Mouse Exon 1.0 ST Affymetrix arrays were scanned using the GeneChip Scanner 3000.
Description RMA expression value derived from Expression Console software
Data processing Microarray data were initially processed using GeneChip Operating Software. DTT data were transferred by Transfer Tool software (Affymetrix). Chip quality and raw microarray data pre-processing were performed according to the Affymetrix guidelines using Expression Console software. The following parameters were checked on the arrays: mean signal, mean background signal and comparison of signal values from the positive controls to the negative. After background subtraction, the data were processed using RMA (All: RMA-Sketch) method and quantile normalization.
 
Submission date Feb 04, 2011
Last update date May 13, 2011
Contact name Marcin Piechota
E-mail(s) marpiech@if-pan.krakow.pl
Phone (+4812) 6623328
Organization name Institute of Pharmacology PAS
Department Molecular Neuropharmacology
Street address Smetna 12
City Krakow
ZIP/Postal code 31-343
Country Poland
 
Platform ID GPL6193
Series (1)
GSE27088 The comparison of gene expression profile in the amygdalae between the wild-type and neuropsin knock-out mice

Data table header descriptions
ID_REF
VALUE RMA signal
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
4304920 3.49425 0.0233749
4304921 1.81054 0.633562
4304922 4.92188 0.00375195
4304923 6.99448 1.2558e-05
4304925 6.46613 2.41097e-05
4304927 2.59745 0.586737
4304928 11.3722 4.68706e-09
4304929 10.5476 3.79516e-06
4304930 5.01133 0.00467608
4304931 5.11781 0.00597126
4304932 4.3764 0.0234088
4304933 1.9315 0.801937
4304934 3.94669 0.109623
4304935 3.27072 0.191769
4304937 9.15075 4.45668e-09
4304938 2.76307 0.0765076
4304939 3.02041 0.293093
4304940 3.79571 0.326744
4304941 5.59223 0.0173199
4304942 8.07815 0.00141841

Total number of rows: 1256831

Table truncated, full table size 31666 Kbytes.




Supplementary file Size Download File type/resource
GSM668596_RP4007_MouseExon_1.0ST_110208.CEL.gz 21.9 Mb (ftp)(http) CEL
GSM668596_RP4007_MouseExon_1.0ST_110208.ppp2.rma-exon-all-dabg.chp.gz 11.7 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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