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Sample GSM660444 Query DataSets for GSM660444
Status Public on Dec 31, 2011
Title 3xTg-HIP-Vehicle-1
Sample type RNA
 
Source name Hippocampus
Organism Mus musculus
Characteristics tissue: Hippocampus
gender: male
genotype/variation: 3xTgAD
age: 18 months
Treatment protocol Male 3xTgAD mice, 14 months of age, were maintained on a 12hr light dark cycle in pathogen free conditions. Animals received food and plain water ad libitum.
Extracted molecule total RNA
Extraction protocol The RNA purification was done using glass bead disruption followed by the RNEasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. The RNA was examined for quantity and quality using an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).
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, 0.5g 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 SentrixMouse Ref-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 = Hippocampus from male 3xTgAD mice, 18 months of age,
Data processing Data was extracted using the Illumina BeadStudio software(v3.4). 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 p-values is included in the supplemental file.
 
Submission date Jan 24, 2011
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)
GSE26836 Amitriptyline-mediated cognitive enhancement in aged 3xTg Alzheimer’s disease mice is associated with neurogenesis and neurotrophic activity

Data table header descriptions
ID_REF
RAW_VALUE raw intensity value from Illumina BeadStudio software
VALUE Z transformation of the natural log of the raw intensity values

Data table
ID_REF RAW_VALUE VALUE
ILMN_1212607
ILMN_1212612 684.8668 1.623910042
ILMN_1212619 76.24017 -0.441442205
ILMN_1212628
ILMN_1212632 73.22632 -0.479387665
ILMN_1212636 1079.75 2.052214973
ILMN_1212637 205.093 0.489541097
ILMN_1212645 112.1573 -0.078283837
ILMN_1212648 144.1835 0.158028228
ILMN_1212653 434.4652 1.195748042
ILMN_1212672 146.7583 0.174680438
ILMN_1212682
ILMN_1212683
ILMN_1212685
ILMN_1212692
ILMN_1212693 94.97556 -0.234721157
ILMN_1212695 70.05585 -0.521029086
ILMN_1212698
ILMN_1212702 3854.789 3.24945313
ILMN_1212703 149.4184 0.191580251

Total number of rows: 25697

Table truncated, full table size 645 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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