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Sample GSM1015334 Query DataSets for GSM1015334
Status Public on Oct 17, 2012
Title sham-4
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
ID_REF
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
ID_REF VALUE RAW_VALUE
ILMN_1212607 -0.54400793 112.7801
ILMN_1212612 1.23151234 851.8239
ILMN_1212619 0.100498566 234.9554
ILMN_1212628
ILMN_1212632 -0.129271949 180.8623
ILMN_1212636 2.038755353 2135.931
ILMN_1212637 0.38288983 324.0764
ILMN_1212645 -0.003627919 208.6833
ILMN_1212648 0.434083964 343.5314
ILMN_1212653 0.986735085 644.6004
ILMN_1212672 0.23309658 273.2526
ILMN_1212682
ILMN_1212683
ILMN_1212685
ILMN_1212692
ILMN_1212693 -0.441996037 126.6731
ILMN_1212695 -0.507283716 117.5967
ILMN_1212698
ILMN_1212702 3.322036159 9209.969
ILMN_1212703 -0.120310419 182.7175

Total number of rows: 25697

Table truncated, full table size 654 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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