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Sample GSM252074 Query DataSets for GSM252074
Status Public on Dec 20, 2007
Title Mouse liver, biological replicate 1
Sample type RNA
 
Source name Mouse liver
Organism Mus musculus
Characteristics C57Bl6 male mice (10-12 weeks old)
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIzol Reagent according to the manufacturerÆs protocol (Gibco BRL, Carlsbad, CA), followed by a cleanup procedure with RNeasy columns (Qiagen, Cologne, Germany).The total RNA quantity and quality was determined using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DW) and the 2100 Bioanalyzer (Agilent, Waldbronn, Germany), respectively. Total RNA profiles of all tested samples were similar with sharp 18S and 28S rRNA peaks on a flat baseline.
Label Biotin
Label protocol Cellular mRNA was reverse transcribed into cDNA (SuperScript Choice System Invitrogen, Carlsbad, CA using oligo-dT primers and a T7 RNA polymerase promoter site). Two ??g of total RNA was used to prepare biotinylated cRNA with IVT labeling kit (Affymetrix, Santa Clara, CA) according to the Genechip expression analysis technical manual 701025 Rev.5. The concentration of labelled cRNA was measured using the NanoDrop ND-1000 spectrophotometer. Labeled cRNA was fragmented in a fragmentation buffer during 35 min at 94??C. The quality of labelled and fragmented cRNA was analysed using the Agilent bioanalyzer 2100.
 
Hybridization protocol Fragmented cRNA was hybridised to mouse 430 2.0 arrays (Affymetrix) during 16h at 45??C.
Scan protocol The arrays were washed and stained in a fluidics station (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.
Description Mouse liver
Data processing All image files were analysed using the affy library of the BioConductor project (no background adjustment, probe-level quantile normalization, and average difference summarization)
 
Submission date Dec 19, 2007
Last update date Aug 28, 2018
Contact name LĂ©on-Charles Tranchevent
E-mail(s) ltranche@esat.kuleuven.be
Organization name Katholieke Universiteit Leuven
Department Departement of Electrical Engineering
Lab ESAT-SCD
Street address Kasteelpark Arenberg 10
City Leuven-Heverlee
ZIP/Postal code B-3001
Country Belgium
 
Platform ID GPL1261
Series (1)
GSE9954 Large-scale analysis of the mouse transcriptome
Relations
Reanalyzed by GSM595377
Reanalyzed by GSE119085

Data table header descriptions
ID_REF Affymetrix probeset identifier
VALUE Normalized signal intensity

Data table
ID_REF VALUE
1415670_at 534.43
1415671_at 1040.83
1415672_at 1296.34
1415673_at 232.4
1415674_a_at 411.54
1415675_at 272.69
1415676_a_at 1577.06
1415677_at 1271.49
1415678_at 818.4
1415679_at 1251.89
1415680_at 338.46
1415681_at 716.94
1415682_at 288.86
1415683_at 1062.6
1415684_at 649.77
1415685_at 622.6
1415686_at 593.89
1415687_a_at 1632.4
1415688_at 1130.57
1415689_s_at 240.71

Total number of rows: 45101

Table truncated, full table size 788 Kbytes.




Supplementary file Size Download File type/resource
GSM252074.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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