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Sample GSM239904 Query DataSets for GSM239904
Status Public on Dec 07, 2007
Title B6_SleepDep_ZT 0_2
Sample type RNA
 
Source name C57BL/6J, sleep deprived, time of sacrifice ZT 0, replicat 2
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 9.417640102
1415671_at 11.21115041
1415672_at 10.60127968
1415673_at 8.047762831
1415674_a_at 9.280549727
1415675_at 8.624396215
1415676_a_at 10.44120526
1415677_at 9.236104447
1415678_at 10.16308764
1415679_at 10.37350137
1415680_at 7.878845129
1415681_at 9.307417258
1415682_at 7.694816263
1415683_at 10.13610381
1415684_at 7.579696395
1415685_at 8.262947379
1415686_at 9.650515868
1415687_a_at 12.66560819
1415688_at 9.859712418
1415689_s_at 7.103600168

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM239904.CEL.gz 6.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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