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Sample GSM1647736 Query DataSets for GSM1647736
Status Public on Apr 04, 2015
Title WCN002_mock_8h_1_mRNA
Sample type RNA
 
Source name Primary cortical neurons, mock-inoculated, 8 hour(s), bioreplicate 1, technical replicate 1
Organism Mus musculus
Characteristics strain: C57Bl/6J
embryonic stage: E15
developmental stage: embryo
tissue: brain
time: 8
virus: mockulum
technical_replicate: 1
biological_replicate: 1
Treatment protocol On day 4, triplicate technical replicates of cortical neurons were mock-inoculated or inoculated with plasmid-derived wild type West Nile virus NY99 clone 382 (WNVWT) or a plasmid-derived isogenic E218A mutant West Nile virus NY99 clone 382 (WNVE218A). After 1 hr of infection at 37oC, virus inoculum was removed. Neurons were then cultured for 0-23 additional hours at 37oC. At 1, 8, 12 and 24 hours after inoculation medium was removed and RNA harvested from adherent neurons using Trizol.
Growth protocol Mouse fetal brain was taken from C57Bl/6J mouse embryos at E15. After removing meninges, cortical tissue was dissociated, filtered and plated in neurobasal medium (with B27 supplement, Glutamax and penicillin/streptomycin) at a density of 5 x 105 cells/well in a poly-D-lysine and laminin coated 24-well dish. Three days after plating (D2), cell medium was replaced with fresh medium.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from Trizol.
Label Cy3
Label protocol Total RNA was labeled according to Agilent’s Quick Amp Labeling protocol as part of the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). Total RNA from each sample was linearly amplified and labeled with Cy3-UTP.
 
Hybridization protocol Hybridization was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.
Scan protocol The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).
Data processing Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). The limma package for R (available on Bioconductor) was used to perform background correction, quantile normalization (normalizeBetweenArrays), and summarization (avereps) to derive a single normalized intensity value per probe. Outlier samples were detected using PCA and by visual inspection of heatmaps, and all data was re-processed after removing outlier samples. All data processing for each of the two biological replicates was performed independently of the other.
 
Submission date Mar 31, 2015
Last update date Aug 31, 2016
Contact name Natalie Heller
E-mail(s) natalie.heller@pnnl.gov
Organization name PNNL
Street address 902 Battelle Blvd.
City Richland
ZIP/Postal code 99354
Country USA
 
Platform ID GPL11202
Series (2)
GSE65575 Modeling Host Responses to Understand Severe Human Virus Infections
GSE67473 Mouse cortical neuron transcriptional response to wild-type West Nile virus (WNV-NY) and mutant virus WNV E218A [mRNA]

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_51_P100034 8.86202568
A_51_P100174 8.933748572
A_51_P100208 10.91648752
A_51_P100289 11.5663774
A_51_P100298 7.709524596
A_51_P100309 7.697794304
A_51_P100327 8.107052423
A_51_P100347 7.726733729
A_51_P100519 7.61283896
A_51_P100537 7.784817314
A_51_P100573 8.654682526
A_51_P100624 7.668366652
A_51_P100625 7.850434465
A_51_P100768 7.783368705
A_51_P100776 7.739549542
A_51_P100787 12.71432745
A_51_P100828 12.12581591
A_51_P100852 7.707936452
A_51_P100991 8.655237336
A_51_P100997 8.684394039

Total number of rows: 39429

Table truncated, full table size 981 Kbytes.




Supplementary file Size Download File type/resource
GSM1647736_WCN002_mock_8h_1_mRNA.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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