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Sample GSM239906 Query DataSets for GSM239906
Status Public on Dec 07, 2007
Title B6_SleepDep_ZT 6_1
Sample type RNA
 
Source name C57BL/6J, sleep deprived, time of sacrifice ZT 6, replicat 1
Organism Mus musculus
Characteristics Strain: C57BL/6J, Gender: male, Age: 12-13 weeks of age, Tissue: whole brain
Extracted molecule total RNA
Extraction protocol Mice were sacrificed by cervical dislocation. RNA from whole brain was isolated and purified with Rneasy Lipid tissue Midi kit (Qiagen) and Dnase treated. Equal amount of total RNA was pooled from 3 mice within each of the 24 experimental groups (3 strains, 2 conditions, 4 ZT = 24 ; in triplicate : 24 * 3 = 72 chips).
Label biotin
Label protocol Target preparations were performed as described by the Affymetrix GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com), and were conducted at the DNA array facility of the University of Lausanne (Switzerland). 3 ug of each pool was used to perform the chiparray experiment according to the Affymetrix Gene Expression procedure.
 
Hybridization protocol Twelve 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 and hybridization quality control were assessed using RACE (Psarros et al., 2005), a web service based on Bioconductor “affy” and “affyPLM” packages (Gautier et al., 2004).
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)
GSE9442 Molecular correlates of sleep deprivation in the brain of three inbred mouse strains in an around-the-clock experiment
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 9.288495587
1415671_at 11.24529949
1415672_at 10.69605307
1415673_at 8.034966224
1415674_a_at 9.339808694
1415675_at 8.847598355
1415676_a_at 10.60545993
1415677_at 9.283975881
1415678_at 10.2724468
1415679_at 10.36605109
1415680_at 7.977799619
1415681_at 9.50599874
1415682_at 7.811444284
1415683_at 9.857631538
1415684_at 7.667200869
1415685_at 8.224499896
1415686_at 10.07202903
1415687_a_at 12.58583427
1415688_at 9.587597337
1415689_s_at 6.962449339

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM239906.CEL.gz 6.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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