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Sample GSM1231466 Query DataSets for GSM1231466
Status Public on Jan 17, 2014
Title Muscle_Saline Control_Replicate-3
Sample type RNA
Source name Muscle_Saline Control
Organism Mus musculus
Characteristics strain: C57BL/6J
gender: female
age: 23 months old
treatment: saline vehicle for 3 days.
tissue: gastrocnemius muscle
Treatment protocol Mice were injected intraperitoneally with 5-Aminoimidazole-4-carboxamide-1-a-D-ribofuranoside (AICAR, Toronto Research Chemicals Inc., Canada) dissolved in saline, 500 mg/kg/day for 3 (ACR3), 7 (ACR7) or 14 (ACR14) days or saline vehicle, for 3 (CTR) days. Thirty-three days after the final injection animals were deeply anesthetized with isofluorane and perfused transcardially with 0.9% NaCl solution. The gastrocnemius muscle and Hippocampus were quickly removed, frozen on dry ice and stored at −80 °C for RNA isolation and microarray analysis.
Growth protocol 23-month old female C57BL/6J mice (Jackson Laboratory, Bar Harbor, ME) were housed under standard conditions, 3 mice per cage, with food and water ad libitum.
Extracted molecule total RNA
Extraction protocol RNA isolation was carried out using the Qiagen RNeasy Mini Kit for animal tissues (Qiagen, Inc., Valencia, CA) following the manufacturer’s instructions. Quantity and quality of the RNA was assessed using the Agilent 2100 Bioanalyzer with RNA 6000 Nano Chips.
Label Streptavidin-Cy3 bound to biotin labeled cRNA.
Label protocol Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5ug of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.
Hybridization protocol Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix MouseRef-8 v2 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.
Scan protocol Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.
Description CTR\-MUS28
Data processing Data was extracted using the Illumina BeadStudio software(v1.6.0). Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std. Complete data including detection scores will be included in the supplemental file.
Submission date Sep 13, 2013
Last update date Jun 22, 2020
Contact name Supriyo De
Organization name NIA-IRP, NIH
Department Laboratory of Genetics and Genomics
Lab Computational Biology & Genomics Core
Street address 251 Bayview Blvd
City Baltimore
State/province Maryland
ZIP/Postal code 21224
Country USA
Platform ID GPL6885
Series (1)
GSE50873 AMPK agonist AICAR improves cognition and motor coordination in young and aged mice

Data table header descriptions
VALUE normalized as described above
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1250052 -0.324264265 0.00251
ILMN_3122480 -0.626915805 0.49499
ILMN_2599935 0.783587541 0
ILMN_2675543 -0.534111084 0.1416
ILMN_2686883 -0.567789187 0.22556
ILMN_2751818 -0.618033776 0.44862
ILMN_2728634 -0.435928513 0.03008
ILMN_3040515 -0.52737995 0.12281
ILMN_2711608 -0.51869902 0.10401
ILMN_1232875 -0.506150219 0.08396
ILMN_1258507 -0.583300546 0.27444
ILMN_2746142 -0.630640892 0.52005
ILMN_1252690 -0.464412652 0.04386
ILMN_2655499 -0.699470589 0.79323
ILMN_1252870 -0.441435797 0.03258
ILMN_1248179 -0.57763119 0.2594
ILMN_2649955 -0.082241199 0.00125
ILMN_2628708 -0.701075098 0.79825
ILMN_3024781 -0.509436762 0.08521
ILMN_2705628 -0.52737995 0.12281

Total number of rows: 25697

Table truncated, full table size 795 Kbytes.

Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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