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Sample GSM1088043 Query DataSets for GSM1088043
Status Public on Mar 18, 2013
Title Mus musculus hippocampus tissue_blast-mTBI_rep5
Sample type RNA
 
Source name male ICR_hippocampus_physical-mTBI from a blast exposure
Organism Mus musculus
Characteristics strain: ICR
gender: male
weight: 30-40g
exposed to: blast-TBI from an explosion
tissue: hippocampus
Treatment protocol Behavioral assessments were initiated 7 days after the animals were exposed to either physical-mTBI, blast-mTBI, or sham-mTBI. This time point was selected based upon prior studies with these models where behavioral deficits were observed to occur from this time point. Mouse cognition and emotional behavior was assessed using the novel object recognition; Y maze; passive avoidance and elevated plus maze paradigms.
Growth protocol Male ICR mice weighing 30–40 g were kept five per cage under a constant 12-h light/dark cycle, at room temperature (22+/-2°C). Food (Purina rodent chow) and water were available ad libitum. Each mouse was used for one experiment. The Ethics Committee of the Sackler Faculty of Medicine approved the experimental protocol (M-09-055, M-07-055), in compliance with the guidelines for animal experimentation of the National Institutes of Health (DHEW publication 85–23, revised, 1995). All experimental manipulations were conducted during the light phase of the cycle.
Extracted molecule total RNA
Extraction protocol After the completion of the behavioral assessments, animals were euthanized and the right hippocampus dissected for total RNA isolation. 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 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 Blast-TBI_5
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; Detection_Pval = Detection Pvalue from Illumina BeadStudio software, (v.3.4.0).
 
Submission date Feb 25, 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 (2)
GSE44625 Changes in mouse cognition and hippocampal gene expression observed in a mild physical- and blast-traumatic brain injury
GSE71850 Blast traumatic brain injury induced cognitive deficits are attenuated by pre- or post-injury treatment with the glucagon-like peptide-1 receptor agonist, exendin-4

Data table header descriptions
ID_REF
VALUE Z_VALUE (Z transformation of the natural log of the raw intensity values)
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1212607 -0.569953078 0.1378446
ILMN_1212612 1.38550331 0
ILMN_1212619 -0.130185592 0
ILMN_1212628
ILMN_1212632 0.040108422 0
ILMN_1212636 2.016599703 0
ILMN_1212637 0.318868897 0
ILMN_1212645 0.283451684 0
ILMN_1212648 0.303283326 0
ILMN_1212653 1.304871252 0
ILMN_1212672 0.176183435 0
ILMN_1212682
ILMN_1212683
ILMN_1212685
ILMN_1212692
ILMN_1212693 -0.405418449 0.01378446
ILMN_1212695 -0.543104665 0.09649123
ILMN_1212698
ILMN_1212702 4.639883988 0
ILMN_1212703 0.086808139 0

Total number of rows: 25697

Table truncated, full table size 589 Kbytes.




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

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