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Sample GSM239847 Query DataSets for GSM239847
Status Public on Dec 07, 2007
Title B_D2_SleepDep_ZT 6_1
Sample type RNA
 
Source name DBA/2J, sleep deprived, time of sacrifice ZT 6, replicat 1, 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 (http://www.affymetrix.com), 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
E-mail(s) mehdi.tafti@unil.ch
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
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE RMA; Log2 normalized expression signal

Data table
ID_REF VALUE
1415670_at 9.06611225
1415671_at 10.6307798
1415672_at 9.232574718
1415673_at 7.057444878
1415674_a_at 8.163963529
1415675_at 8.035835718
1415676_a_at 9.898555587
1415677_at 8.425513536
1415678_at 9.373606654
1415679_at 8.964846904
1415680_at 7.08197436
1415681_at 8.733802884
1415682_at 7.477867393
1415683_at 8.850256161
1415684_at 7.101486028
1415685_at 6.510177509
1415686_at 9.384596994
1415687_a_at 11.56154955
1415688_at 8.772343646
1415689_s_at 7.134636272

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM239847.CEL.gz 5.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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