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Sample GSM1504426 Query DataSets for GSM1504426
Status Public on Mar 27, 2015
Title Lung-d3_SeV-1b
Sample type RNA
 
Source name whole lung, SeV post-infection day 3, rep 1, array strip B
Organism Mus musculus
Characteristics strain: C57BL/6J
time: 3 days post-infection
infection: active Sendai virus
gender: Male
Treatment protocol Sendai virus (SeV), strain 52, was obtained from American Type Culture Collection and stored at -70°C. Mice were inoculated with SeV or an equivalent amount of UV-inactivated SeV (SeV-UV) intranasally. 3-5 week old male C57BL/6J mice were obtained from Jackson Laboratory. Mice were sacrificed post-infection day 3, and lungs were harvested, right for RNA, left for histology and other studies (see Kim et al, 2008, PMID:18488036).
Growth protocol Mice were maintained under pathogen-free conditions, and all study protocols were approved by the Washington University Animal Studies Committee.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using QIAGEN RNeasy kit per manufacturer's protocol. Quality control was performed with Agilent Bioanalyzer.
Label biotin
Label protocol Biotinylated aRNA were prepared using the Illumina TotalPrep Kit (Ambion) per manufacturer's protocol.
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol except for adding output of raw array data for beadlevel analyses
Description Strip B from array and sample B6.3.S.3691.2 each BeadChip consists of two strips (A & B).
Data processing Hybridization and scanning of BeadChip arrays was performed according to the manufacturer’s instructions, using BeadStudio 3.0 software (Illumina). In order to perform bead-level analysis, raw data is exported from BeadStudio. Microarray normalization and statistical analysis was performed using packages from the Bioconductor project executed in the R programming environment. Raw bead-level intensity data was imported using functions from the beadarray package, including background correction. Each Mouse-WG6 v2 BeadChip array consists of two strips. Due to potential variation in the data from the two different strips (see Shi et al. (2009) [PMID:19903361]), we treated the individual strips from each sample separately through bead-summarization. Thus, for each strip, low-level analysis and quality control was performed using functions from the beadarray package (see Ritchie et al. (2011) [PMID:22144879]). The BASH algorithm was then applied to the raw data to mask beads affected by large spatial artifacts, followed by bead-type summarization, including removal of outlier beads. Summarized data were Log2-transformed, followed by quantile normalization.
 
Submission date Sep 15, 2014
Last update date Mar 27, 2015
Contact name Anand Champak Patel
E-mail(s) [email protected]
Organization name Washington University School of Medicine
Department Pulmonary/Critical Care Medicine
Lab Patel
Street address Campus Box 8116, 660 S. Euclid Ave.
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
 
Platform ID GPL17543
Series (1)
GSE61437 Virus-Induced Airway Disease in Mice (C57BL/6J, d3)

Data table header descriptions
ID_REF
VALUE log2 quantile normalized values
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1212602 7.265496783 0
ILMN_1212603 6.309942953 0.947598253
ILMN_1212605 10.64962186 0
ILMN_1212607 6.757380284 0.155021834
ILMN_1212612 7.585156185 0
ILMN_1212614 6.372053178 0.890829694
ILMN_1212619 7.641865091 0
ILMN_1212623 6.884930906 0.063318777
ILMN_1212625 10.5030383 0
ILMN_1212626 6.994602283 0.027292576
ILMN_1212628 6.547682317 0.540393013
ILMN_1212632 7.056380645 0.013100437
ILMN_1212633 6.736307271 0.180131004
ILMN_1212636 11.25715096 0
ILMN_1212637 8.013123701 0
ILMN_1212638 11.87150852 0
ILMN_1212639 8.564769323 0
ILMN_1212644 6.597010701 0.409388646
ILMN_1212645 7.131343916 0
ILMN_1212646 10.10499986 0

Total number of rows: 46237

Table truncated, full table size 1498 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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