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Sample GSM2436375 Query DataSets for GSM2436375
Status Public on Feb 27, 2019
Title Liver, LA2_30mpk, rep1
Sample type RNA
 
Source name Liver, LA2_30mpk, rep1
Organism Mus musculus
Characteristics tissue: Liver
strain: C57BL/6
age: 12 weeks
Treatment protocol At 12 weeks of age, lean C57BL/6 mice were fasted by removing food at 7:30 am and then dosed with vehicle (0.25% MC, 5% Tween-80, 0.02% SDS) or AMPK activators by oral gavage at around 9:30 am, and kept sedentary for the remainder of the study period. For the exercise arm, mice were put on a treadmill (Columbus Instruments International, OH) for exercise with speed set at 10 meter/min. Mice exercised for 30 min followed by 30 min rest and the total running distance was 1300 meters.
Growth protocol Male lean C57BL/6 were purchased from Taconic (Hudson, NY) at 8 weeks of age and maintained on chow diet (Teklad 7012, Research Diets, Inc., New Brunswick, NJ) with free access to water in a 12 h light/12 h dark cycle.
Extracted molecule total RNA
Extraction protocol Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.
Label biotin
Label protocol The reverse transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency. The labeled molecules are biotinylated-cDNA.
 
Hybridization protocol GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.
Scan protocol Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.
Description Mice were treated with a single dose of the long acting AMPK activator, LA2, at 30mpk and 6 hours post dose Liver was taken for RNA profiling.
Data processing Gene expression data were processed using the Robust Multiarray Average (RMA) pipeline and one-way ANOVA analysis was performed to obtain fold change, raw p values, and False Discovery Rate Benjamini & Hochberg (FDR_BH) corrected p values using the Array Studio Software (Omicsoft Corporation, Cary, NC). Probe sets had to pass a pre-filter of Affymetrix MAS5 present call p-value < 0.05 in > 50% of the samples, per treatment group, to qualify for further analysis. Average fold changes between 1) exercise and sedentary (vehicle treated) or 2) compound and vehicle treatment groups (both sedentary) were generated with the sedentary vehicle group serving as baseline.
 
Submission date Dec 21, 2016
Last update date Feb 28, 2019
Contact name eric muise
E-mail(s) eric_muise@merck.com
Organization name Merck
Department Genetics and Pharmacogenomics
Street address 33 Ave Louis Pasteur
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL9734
Series (1)
GSE92719 Pharmacological AMPK activation induces transcriptional responses congruent to exercise in skeletal and cardiac muscle, adipose tissues and liver

Data table header descriptions
ID_REF
VALUE Log2 transformed RMA intensity.

Data table
ID_REF VALUE
100079054_TGI_at 3.5187
100079056_TGI_at 3.0962
100079058_TGI_at 2.8376
100079059_TGI_at 2.2413
100079060_TGI_at 2.6802
100079061_TGI_at 7.7255
100079062_TGI_at 2.5263
100079064_TGI_at 6.4544
100079065_TGI_at 5.4942
100079066_TGI_at 2.2711
100079067_TGI_at 3.6161
100079068_TGI_at 4.6839
100079069_TGI_at 3.5549
100079070_TGI_at 7.4827
100079071_TGI_at 2.0887
100079072_TGI_at 2.147
100079073_TGI_at 3.3925
100079074_TGI_at 3.2364
100079075_TGI_at 9.8682
100079076_TGI_at 6.3114

Total number of rows: 38385

Table truncated, full table size 897 Kbytes.




Supplementary file Size Download File type/resource
GSM2436375__52048700763414070813414331844072.CEL.gz 3.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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