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Sample GSM1846755 Query DataSets for GSM1846755
Status Public on Aug 05, 2016
Title Exendin4 Pre-TBI_replicate 3
Sample type RNA
 
Source name Hippocampus_EX-4 PreTBI_Day 3
Organism Mus musculus
Characteristics strain: ICR
gender: Male
tissue: Brain
tissue: Hippocampus
Treatment protocol Hippocampal brain gene expression was examined on day 3 and day 14 (Experiment GSE44625) after male ICR mice (30-40 g) underwent a blast traumatic brain injury (B-TBI) or sham procedure. Animals received 3.5 pM/kg/min (21ug/kg/day) Exendin-4 using Alzet micro-osmotic pumps either as a pre-treatment to the blast injury 48 hours before (Ex-4 pre-TBI) or as a post-treatment 2 hours after the blast injury (Ex-4 post-TBI) and were evaluated at Day 3 post-blast. Animals in a previous data set on Day 14 (GSE44625) were administered Ex-4 as a pre-treatment.
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 and water were available ad libitum. Each mouse was used for one experiment and for one time point only. The Ethics Committee of the Sackler Faculty of Medicine approved the experimental protocol (M-11-086), in compliance with the guidelines for animal experimentation of the National Institutes of Health (DHEW publication 85-23, revised, 1995). The numbers of animals per treatment group for the assessment of neurodegeneration; gene expression and animal cognition were selected based upon experience from prior studies. All attempts were made to minimize both the numbers of mice used for our studies and their suffering. All experimental manipulations were conducted during the light phase of the light/dark cycle. At the time of animal euthanasia, a two stage method approved by the Sackler Faculty of Medicine Ethics Committee was employed; animals were terminally anesthetized with Isoflurane, followed by decapitation.
Extracted molecule total RNA
Extraction protocol RNA was extracted from dissected hippocampi using the RNeasy kit (Qiagen, Valencia, CA) using the standard manufactures protocol. Samples were assessed for quality and quantity using an Agilent 2100 Bioanlyzer with RNA 6000 Nano Chips, (Aligent technologies).
Label biotin
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 Human-Ref8 v3 Expression Bead Chips (Illumina, San Diego, CA). Each BeadChip has ~22,000 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 DRUG_INJ_BL_3
Hippocampus_Exendin4 Pre-TBI_replicate 3
Data processing Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue 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 is supplied.
 
Submission date Aug 07, 2015
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)
GSE71846 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 [Day 3 dataset]
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 Detection_Pval = Detection Pvalue from Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0.
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1212607 -0.775555488 0.31454
ILMN_1212612 1.089129806 0
ILMN_1212619 0.091858945 0
ILMN_1212628 -0.850975912 0.49123
ILMN_1212632 0.019025811 0
ILMN_1212636 2.070793622 0
ILMN_1212637 0.550181527 0
ILMN_1212645 1.072215448 0
ILMN_1212648 0.429632801 0
ILMN_1212653 0.982068185 0
ILMN_1212672 0.37200245 0
ILMN_1212682 -0.828910923 0.42481
ILMN_1212683 -0.91176257 0.72306
ILMN_1212685 -0.991744825 0.95865
ILMN_1212692 -0.652716475 0.16667
ILMN_1212693 0.073418393 0
ILMN_1212695 -0.280582274 0.00752
ILMN_1212698 -0.958406557 0.89098
ILMN_1212702 3.204112263 0
ILMN_1212703 -0.18952308 0.00251

Total number of rows: 25697

Table truncated, full table size 780 Kbytes.




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

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