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Sample GSM1231438 Query DataSets for GSM1231438
Status Public on Jan 17, 2014
Title Hippocampus_AICAR-14days_Replicate-3
Sample type RNA
 
Source name Hippocampus_AICAR-14days
Organism Mus musculus
Characteristics strain: C57BL/6J
gender: female
age: 23 months old
treatment: 5-Aminoimidazole-4-carboxamide-1-a-D-ribofuranoside dissolved in saline, 500 mg/kg/day for 14 days
tissue: hippocampus
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 ACR14_HIP3
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
ID_REF
VALUE normalized as described above
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1250052 -0.361890746 0.01003
ILMN_3122480 -0.740930236 0.75815
ILMN_2599935 0.494154746 0
ILMN_2675543 -0.719403201 0.69674
ILMN_2686883 -0.248524874 0
ILMN_2751818 -0.092018176 0
ILMN_2728634 -0.438315239 0.02506
ILMN_3040515 -0.575145682 0.20301
ILMN_2711608 -0.586414803 0.23183
ILMN_1232875 -0.501096198 0.0614
ILMN_1258507 -0.523443367 0.09524
ILMN_2746142 -0.718692871 0.69424
ILMN_1252690 -0.512800994 0.07519
ILMN_2655499 -0.651892905 0.44737
ILMN_1252870 -0.243912512 0
ILMN_1248179 -0.516336971 0.08521
ILMN_2649955 -0.318669118 0.00627
ILMN_2628708 -0.650557572 0.44486
ILMN_3024781 -0.568315659 0.1817
ILMN_2705628 -0.557843261 0.1604

Total number of rows: 25697

Table truncated, full table size 781 Kbytes.




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

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