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Status |
Public on Jan 17, 2014 |
Title |
Hippocampus_AICAR-14days_Replicate-4 |
Sample type |
RNA |
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Source name |
Hippocampus_AICAR-14days
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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
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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.
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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.
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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.
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Label |
Streptavidin-Cy3 bound to biotin labeled cRNA.
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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.
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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.
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Scan protocol |
Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.
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Description |
ACR14_HIP8
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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.
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Submission date |
Sep 13, 2013 |
Last update date |
Jun 22, 2020 |
Contact name |
Supriyo De |
Organization name |
NIA-IRP, NIH
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Department |
Laboratory of Genetics and Genomics
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Lab |
Computational Biology & Genomics Core
|
Street address |
251 Bayview Blvd
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City |
Baltimore |
State/province |
Maryland |
ZIP/Postal code |
21224 |
Country |
USA |
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Platform ID |
GPL6885 |
Series (1) |
GSE50873 |
AMPK agonist AICAR improves cognition and motor coordination in young and aged mice |
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