|
| Status |
Public on Aug 04, 2015 |
| Title |
Ma_hi_#3_9482913022_F |
| Sample type |
RNA |
| |
|
| Source name |
Spleen from male mice
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6 Foxp3-GFP-DTR-CD90.1
tissue: Spleen
gender: male
cell type: CD4+Foxp3-CD5high
|
| Treatment protocol |
Mice were untreated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spleen was harvested directly after euthanasia of mice and cells were FACS purified.
|
| Label |
biotin
|
| Label protocol |
The NuGEN Ovation Pico WTA System (linear isothermal DNA amplification process) was used to generate single-stranded cDNA from small input amounts of 2.5 ng RNA. Labeled cRNA was prepared according to Nugene Encore BiotinIL Module.
|
| |
|
| Hybridization protocol |
1.5 µg of cDNA were hybridized for 17hrs at 55.4 °C on Illumina Mouse WG-6-Microarray
|
| Scan protocol |
Illumina iSCAN-Scanner according to Std Illumina Scanning Protocol Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide). Microarray scanning was done using an iScan array scanner
|
| Description |
Replicate 3
|
| Data processing |
Microarray scanning was done using an iScan array scanner. Data extraction was done for all beads individually, and outliers are removed when the absolute difference to the median is greater than 2.5 times MAD(2.5 Hampelís method). All remaining bead level data points are then quantile normalized [1]. As test for significance the studentís t-test is used on the bead expression values of the two groups of interest. In the case of significance of expression against background we tested for greater than all negative beads for this sample and in the case of comparing separate groups we tested for inequality of the means of the groups. In both cases Benjamini-Hochberg correction [2] was applied to the complete set of p-values of all 48107 ProbeIDs on the chip. The average expression value is calculated as mean of the measured expressions of beads together with the standard deviation of the beads. [1] Probe Level Quantile Normalization of High Density Oligonucleotide Array Data, Ben Bolstad, Division of Biostatistics, University of California, Berkeley December 2001 [2] Y. Benjamini and Y. Hochberg (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B, Vol. 57, 289ñ300.
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| |
|
| Submission date |
Jun 23, 2015 |
| Last update date |
Aug 04, 2015 |
| Contact name |
Michael Delacher |
| E-mail(s) |
[email protected]
|
| Phone |
+49 6131 17 6574
|
| Organization name |
University Medical Center of the Johannes Gutenberg-University Mainz
|
| Department |
Institute for Immunology
|
| Lab |
Immunology
|
| Street address |
Langenbeckstrasse 1
|
| City |
Mainz |
| State/province |
Rhineland-Palatinate |
| ZIP/Postal code |
55131 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17543 |
| Series (1) |
| GSE70154 |
The contained self-reactive peripheral T cell repertoire: size, diversity and cellular composition |
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