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Sample GSM2063026 Query DataSets for GSM2063026
Status Public on Mar 01, 2016
Title PFC PolyI:C offspring, biological replicate 3
Sample type RNA
Source name C57BL/6 mouse Prefrontal Cortex - frozen brain tissue - POLYI:C
Organism Mus musculus
Characteristics strain: C57BL/6N
prenatal exposure: PolyI:C
age: 12 weeks
tissue: brain
tissue region: medial prefrontal cortex (mPFC)
Treatment protocol C57BL/6 mice were treated with the synthetic viral mimetic poly(I:C) (5 mg/kg, i.v.) or control (saline, i.v.) solution on gestation day 17. Offspring were subjected to cognitive and behavioral testing in adulthood, and then whole genome gene expression analysis with Affymetrix Microarray and subsequent q-PCR validation were performed on the Prefrontal Cortex.
Extracted molecule total RNA
Extraction protocol [Tissue extraction protocol] The brains from adult offspring (12 weeks) were rapidly extracted from the skull (within < 20 s) and placed on an ice-chilled plate. This was followed by preparing 1-mm coronal brain sections using razorblade cuts and subsequent micro-dissection of the brain areas of interest. We dissected We dissected the medial prefrontal cortex (mPFC, including anterior cingulate, prelimbic and dorsal parts of the infralimbic cortices; bregma: +2.3 to +1.3 mm) . Brain specimens were collected in 96-well microtiter plates kept on dry ice and allowed to freeze before storage at −80°C until further use. Total DNA and RNA were isolated using the Qiagen AllPrep DNA and RNA Mini kit. Genome-wide gene expression analyses were performed using Affymetrix microarray assays (Mouse Gene 1.1 ST Array Strips on GeneAtlas platform), following the 3’IVT one cycle labelling.
Total DNA and RNA were isolated using the Qiagen AllPrep DNA and RNA Mini kit following the manufacturers' instructions
Label biotin
Label protocol Gene expression microarray assays were performed using Mouse Gene 1.1 ST Array Strips on GeneAtlas platform (Affymetrix), following the 3’IVT one cycle labeling and amplification protocol described in the Affymetrix GeneChip Expression Analysis Technical Manuals and in the GeneAtlas™ WT Expression Kit User Manual. In detail, to synthesize First-Strand cDNA, 250ng RNA were reverse-transcribed with the Gene Atlas 3’IVT Express Kit or WT Expression Kit (Affymetrix, Santa Clara, CA, USA) using T7 oligo(dT) primer. Second-Strand cDNA synthesis was carried out using DNA polymerase and RNase H to simultaneously degrade RNA and synthesize second-strand cDNA. This step was followed by the in vitro transcription using IVT Labelling Master Mix to generate multiple copies of biotin-modified antisense-RNA (aRNA) from the double-stranded cDNA templates. Subsequently strand DNA was purified to remove unincorporated NTPs, salts, enzymes and inorganic phosphate.
Hybridization protocol Labelled cDNA (10ug) was then fragmented and 5.5µg were hybridized onto Mouse Gene 1.1 ST Array Strips. The reactions of hybridation, fluidics and imaging were performed on the Affymetrix Gene Atlas instrument according to the manufacturer’s protocol.
Scan protocol GeneChips were scanned using theGeneAtlas Platform following the manufacturers' instructions.
Description Gene expression data in PolyI:C offspring
sample 28 GD17 PF
Data processing Affymetrix CEL files were imported into Partek Genomics Suite version 6.6 for data visualization and statistical testing. Quality control assessment was performed using Partek Genomic Suite 6.6. All samples passed the criteria for hybridization controls, labelling controls and 3’/5’ Metrics. Background correction was conducted using Robust Multi-strip Average (RMA) (Irizarry et al, 2003) to remove noise from auto fluorescence. After background correction, normalization was conducted using Quantiles normalization (Bolstad et al, 2003) to normalize the distribution of probe intensities among different microarray chips. Subsequently, a summarization step was conducted using a linear median polish algorithm (Tukey, 1977) to integrate probe intensities in order to compute the expression levels for each gene transcript. Upon data upload, pre-processing of CEL data for the complete data set [total of twelve samples; six biological replicates per sample for vehicle, six biological replicates for GD17 Poly(I:C)] was performed using ANOVA to assess treatment effects.
Submission date Feb 16, 2016
Last update date Mar 01, 2016
Contact name Juliet Richetto
Organization name University of Zurich - Vetsuisse
Department Institute for Pharmacology and Toxicology
Street address Winterthurerstrasse 260
City Zurich
ZIP/Postal code 8057
Country Switzerland
Platform ID GPL11533
Series (2)
GSE77972 Expression data from adult mouse Prefrontal Cortex following prenatal infection
GSE77973 Expression data from adult mouse brain regions following prenatal infection

Data table header descriptions
VALUE RMA values

Data table
10338001 9.99337
10338002 4.94098
10338003 8.60434
10338004 7.97697
10338005 2.52013
10338006 2.84436
10338007 3.14838
10338008 3.61649
10338009 5.8098
10338010 2.54762
10338011 4.67928
10338012 2.6375
10338013 2.34215
10338014 2.42493
10338015 2.3391
10338016 5.50991
10338017 11.1751
10338018 5.12981
10338019 4.19344
10338020 5.81823

Total number of rows: 35556

Table truncated, full table size 586 Kbytes.

Supplementary file Size Download File type/resource 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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