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| Status |
Public on Nov 03, 2015 |
| Title |
stimulated subject 262_control |
| Sample type |
RNA |
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| Source name |
whole blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: whole blood
gender: female
stimulus: stimulated
sample type: control
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from whole blood collected in PAXgene Blood RNA tubes using the PAXgene Blood RNA Kit (PreAnalytiX GmbH, Hombrechtikon, Switzerland).
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| Label |
biotin
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| Label protocol |
Sample labeling was performed using the Illumina TotalPrep RNA Amplification Kit (Ambion, TX, USA) according to the manufacturer's instructions.
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| Hybridization protocol |
Biotin-labeled, amplified material was hybridized to Illumina Human-HT-12 v3 and v4 BeadChips, according to the manufacturer's instructions (Illumina, Inc., San Diego, CA, USA; 11322355 Rev. A, 11286331 Rev. A).
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| Scan protocol |
Microarrays were scanned on the Illumina Bead Array Reader (Illumina, Inc., San Diego, CA) with default outlier detection according to the manufacturer's instructions and summarized raw probe intensities were exported using Illumina’s GenomeStudio.
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| Description |
subject 262
Sample 282
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| Data processing |
Microarray expression analysis was performed in R (http://www.r-project.org/). All 29,075 probes present on both microarrays (excluding X and Y chromosomes as well as cross-hybridizing probes) were first filtered by an Illumina detection P value of 0.05 in at least 50% of the samples, leaving 11,994 expressed probes for further analysis. Subsequently, each transcript was transformed and normalized through variance stabilization and normalization (VSN). Filtered data was controlled for confounding by batch effects or unknown factors using Surrogate Variable Analysis with the sva package in Bioconductor.
Raw and processed data are available on the series record. Processed data contains the VSN normalized and transformed signal.
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| Submission date |
Jan 13, 2015 |
| Last update date |
Nov 03, 2015 |
| Contact name |
Janine Arloth |
| Organization name |
Max Planck Institute of Psychiatry
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| Street address |
Kraepelinstr. 2-10
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| City |
Munich |
| ZIP/Postal code |
80804 |
| Country |
Germany |
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| Platform ID |
GPL10558 |
| Series (1) |
| GSE64930 |
Dexamethasone stimulated gene expression in peripheral blood |
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| Supplementary data files not provided |
| Processed data are available on Series record |
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