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Sample GSM1015335 Query DataSets for GSM1015335
Status Public on Oct 17, 2012
Title sham-5
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: vehicle only (sham)
Treatment protocol Mice were treated for 7 days with the just vehicle, a saline and dimethyl sulfoxide (DMSO) mixture and delivered from a subcutaneously implanted ALZET Micro-osmotic pump (Model 1007D, Alzet, Cupertino, CA). Mice were placed into the mTBI equipment on day 3 but no weight was dropped.
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 while being treated with vehicle only.
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 (3)
GSE41345 Exendin-4, a glucagon-like peptide-1 receptor agonist prevents mTBI-induced changes in hippocampus gene expression and memory deficits in mice
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
VALUE Z_VALUE (Z transformation of the natural log of the raw intensity values)
RAW_VALUE raw intensity value from Illumina BeadStudio software.

Data table
ILMN_1212607 -0.538101276 118.4152
ILMN_1212612 1.432124532 1153.61
ILMN_1212619 -0.009842996 218.0145
ILMN_1212632 0.0366061 230.0347
ILMN_1212636 2.181586078 2742.432
ILMN_1212637 0.268990908 300.8868
ILMN_1212645 1.01614833 713.3847
ILMN_1212648 0.468384858 378.8421
ILMN_1212653 1.04791136 740.0522
ILMN_1212672 0.276557838 303.529
ILMN_1212693 -0.143227098 186.8761
ILMN_1212695 -0.585107725 112.1553
ILMN_1212702 3.794370561 17677.66
ILMN_1212703 -0.158074795 183.6975

Total number of rows: 25697

Table truncated, full table size 653 Kbytes.

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

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