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Sample GSM239838 Query DataSets for GSM239838
Status Public on Dec 07, 2007
Title B_B6_Control_ZT 6_1
Sample type RNA
 
Source name C57BL/6J, control, time of sacrifice ZT 6, replicat 1, Brain
Organism Mus musculus
Characteristics Strain: C57BL/6J, 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 9.066072152
1415671_at 10.65611334
1415672_at 9.298657653
1415673_at 7.120149836
1415674_a_at 8.217845223
1415675_at 7.952364458
1415676_a_at 9.864206162
1415677_at 8.583253527
1415678_at 9.496216394
1415679_at 9.309346654
1415680_at 7.072475927
1415681_at 8.665198164
1415682_at 7.238678623
1415683_at 8.612819069
1415684_at 6.882294762
1415685_at 7.352042844
1415686_at 9.475286242
1415687_a_at 11.59297455
1415688_at 8.651036886
1415689_s_at 6.686667219

Total number of rows: 45101

Table truncated, full table size 1025 Kbytes.




Supplementary file Size Download File type/resource
GSM239838.CEL.gz 5.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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