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Sample GSM239848 Query DataSets for GSM239848
Status Public on Dec 07, 2007
Title B_D2_SleepDep_ZT 6_2
Sample type RNA
Source name DBA/2J, sleep deprived, time of sacrifice ZT 6, replicat 2, Brain
Organism Mus musculus
Characteristics Strain: DBA/2J, Gender: male, Age: 12-13 weeks of age, Tissue: whole brain
Extracted molecule total RNA
Extraction protocol RNA was isolated from whole brain and liver by a commercial RNA extraction kit (RNAXEL, Eurobio), treated with Dnase and cleaned using RNeasy columns (Qiagen). Equal amount of total RNA was pooled from 3 mice within each of the 6 experimental groups (3 strains, 2 conditions = 6 ; in triplicate : 6 * 3 = 18 chips) for both brain and liver ( 36 chips in total).
Label biotin
Label protocol Target preparation were performed as described by the Affymetrix GeneChip Expression Analysis Technical Manual (, and were conducted at the Genomics Platform of the NCCR Frontiers in Genetics at the University of Geneva (Switzerland) . Equal quantities of total RNA from three individual mice of each strain were pooled. We generated a hybridization mixture containing 15 ug of biotinylated cRNA according to the protocols provided by Affymetrix.
Hybridization protocol Fifteen micrograms of biotinylated cRNA from each sample were fragmented and hybridized to GeneChip Mouse 430 2.0 arrays, according to standard procedures. Washing and staining was performed using the EuGE-WS2v5 protocol.
Scan protocol Scanning was done on an Affymetrix GeneChip Scanner 7G.
Description none
Data processing Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).
Submission date Oct 26, 2007
Last update date Aug 28, 2018
Contact name Mehdi Tafti
Phone +41216923971
Organization name University of Lausanne
Department CIG
Street address Genopode
City Lausanne
ZIP/Postal code 1015
Country Switzerland
Platform ID GPL1261
Series (2)
GSE9441 The effect of sleep deprivation on gene expression in the brain and the liver of three inbred mouse strains
GSE9444 Sleep deprivation and the brain
Reanalyzed by GSE119085

Data table header descriptions
VALUE RMA; Log2 normalized expression signal

Data table
1415670_at 8.791339878
1415671_at 10.4928632
1415672_at 9.007147933
1415673_at 6.644913665
1415674_a_at 7.83668696
1415675_at 7.760136127
1415676_a_at 9.829635129
1415677_at 8.457644041
1415678_at 9.169898661
1415679_at 8.762585795
1415680_at 6.824395597
1415681_at 8.56778063
1415682_at 7.287232677
1415683_at 8.626905569
1415684_at 6.57271488
1415685_at 5.516987138
1415686_at 9.150958129
1415687_a_at 11.48735187
1415688_at 8.480010634
1415689_s_at 6.456616237

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.

Supplementary file Size Download File type/resource
GSM239848.CEL.gz 6.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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