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Sample GSM1504109 Query DataSets for GSM1504109
Status Public on Sep 01, 2015
Title pancreas-Stat1tg-2
Sample type RNA
 
Source name mouse pancreas obtained at baseline
Organism Mus musculus
Characteristics strain: C57BL/6J
gender: Male
genotype: Stat1-tg
Treatment protocol Mice were untreated and uninfected.
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 mouse pancreas gene expression, baseline, Stat1-Transgenic, C57BL/6J, male.
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 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. 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 Sep 01, 2015
Contact name Anand Champak Patel
E-mail(s) acpatelmd@gmail.com
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 GPL6481
Series (2)
GSE61414 Pancreatic Gene Expression from Wild-Type, Stat1-Transgenic, and Stat1-CC-Transgenic Mice
GSE61421 PARP9 and DTX3L in Antiviral Host Defense

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

Data table
ID_REF VALUE Detection Pval
10243 3.659022011 0
10280 2.961814647 0
10575 4.068362497 0
20048 3.211946014 0
20296 11.12819712 0
20343 2.782324715 0
20373 3.057683728 0
20431 7.341779709 0
50014 2.324334008 0.191157347
50017 2.385466403 0.119635891
50019 6.692202168 0
50020 2.534675924 0.035110533
50022 2.129487821 0.609882965
50025 2.433907324 0.084525358
50026 2.190049832 0.451235371
50035 2.323839133 0.191157347
50037 2.191140249 0.44993498
50039 9.065578675 0
50040 2.158358665 0.535760728
50041 3.701095584 0

Total number of rows: 46643

Table truncated, full table size 1374 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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