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Sample GSM999812 Query DataSets for GSM999812
Status Public on Feb 28, 2013
Title SA.CTR.0.R2
Sample type RNA
 
Source name S727A STAT1 mouse fibroblasts, no interferon, siCtrl, replicate 2
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: S727A STAT1
sirna: control siRNA
agent: untreated
cell type: fibroblast
replicate: 2
Treatment protocol mouse interferon gamma, 10 ng/ml final concentration
Growth protocol DMEM, 10% FCS, pen+strep
Extracted molecule total RNA
Extraction protocol Trizol
Label Cy3
Label protocol Cy3
 
Hybridization protocol Agilent's SurePrint G3 Mouse GE 8x60K Microarray, (Agilent Microarray Design ID 028005).RNA quality was checked on RNA 6000 Nano chips using a Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA). Agilent’s Low Input Quick Amp Labeling Kit, one-color was used to generate fluorescent cRNA. The amplified cyanine 3-labeled cRNA samples were then purified using Promega’s SV Total RNA Isolation System and hybridized to Agilent Whole Mouse Genome Microarrays, 8x60K.
Scan protocol Agilent Scanner, according to the standard protocol of the manufacturer
Description SAMPLE 5
Data processing Further analyses were performed using Bioconductor rooted in the statistical computing environment R. The raw intensities were imported into Bioconductor and further processed with the limma package. Quality Controls were performed using the arrayQualityMetrics package. The outlier array #10 [SA.CDK.gamma.R3] was removed from subsequent analysis. Normalization between arrays was performed using the quantile method, duplicate probes were averaged and a linear model also including a batch effect between Biological Replicates 1 and 2&3 was fitted due to a batch effect shown by the QA PCA plots. P-values were adjusted for multiple testing using the Benjamini & Hochberg method.
 
Submission date Sep 10, 2012
Last update date Feb 28, 2013
Contact name Pavel Kovarik
E-mail(s) pavel.kovarik@univie.ac.at
Organization name University of Vienna
Department Max F. Perutz Laboratories
Street address Dr. Bohr-Gasse 9
City Vienna
ZIP/Postal code 1030
Country Austria
 
Platform ID GPL10787
Series (1)
GSE40728 Role of CDK8 in interferon-gamma-induced gene expression

Data table header descriptions
ID_REF
VALUE Limma quantile-normalized log2 intensities with averaged duplicates

Data table
ID_REF VALUE
A_30_P01017425 8.59
A_30_P01017426 7.08
A_30_P01017427 6.25
A_30_P01017428 9.05
A_30_P01017429 5.68
A_30_P01017430 5.74
A_30_P01017431 6.60
A_30_P01017432 7.44
A_30_P01017433 7.54
A_30_P01017434 8.09
A_30_P01017435 5.15
A_30_P01017436 6.33
A_30_P01017437 10.11
A_30_P01017438 5.58
A_30_P01017439 8.67
A_30_P01017440 5.07
A_30_P01017441 5.58
A_30_P01017442 9.31
A_30_P01017443 11.48
A_30_P01017444 5.48

Total number of rows: 55681

Table truncated, full table size 1047 Kbytes.




Supplementary file Size Download File type/resource
GSM999812_US84903604_252800513901_S01_GE1_107_Sep09_2_1.txt.gz 3.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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