|
| Status |
Public on Oct 17, 2012 |
| Title |
Ex-4-mTBI-1 |
| Sample type |
RNA |
| |
|
| Source name |
Mus musculus hippocampus tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Hippocampus
gender: Male
strain: ICR
weight: 30–40 g
treatment protocol: mice subjected to mTBI induced by weight drop injury while being treated with EX-4 (Ex-4/mTBI)
time: 14 days following mTBI
|
| Treatment protocol |
Mice were treated for 7 days with the peptide Ex-4 dissolved in an equal volume of saline and dimethyl sulfoxide (DMSO) mixture and delivered from a subcutaneously implanted ALZET Micro-osmotic pump (Model 1007D, Alzet, Cupertino, CA) at a rate of 3.5 pM/kg/min. mTBI was induced on day 3 of treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using the Qiagen RNeasy Mini Kit (Qiagen, Inc. Valencia CA) following the manufacturer's specifications. Quantity and quality of the RNA was assessed with the Agilent 2100 Bioanalyzer using 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, 0.5g 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 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 |
Hippocampus tissue of mice subjected to mTBI while being treated with EX-4.
|
| Data processing |
Data was extracted using the Illumina BeadStudio software(v3.4.0). 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 are included in the supplementary file linked to the Series record.
|
| |
|
| Submission date |
Oct 04, 2012 |
| 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) |
| GSE41345 |
Exendin-4, a glucagon-like peptide-1 receptor agonist prevents mTBI-induced changes in hippocampus gene expression and memory deficits in mice |
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