|
| Status |
Public on Oct 28, 2015 |
| Title |
Pdpn pos3 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse mTECs
|
| Organism |
Mus musculus |
| Characteristics |
tra specificity: Pdpn positive mTECs
cell type: FACS isolated medullary thymic epithelial cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of primary sorted mTECs was isolated and purified using the High Pure RNA Isolation Kit (Roche Diagnostics) according to the manufacturers` protocol. Quality control was performed using Agilent Bioanalyser.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled cRNA for hybridization was prepared according to Illumina`s recommended sample labeling procedure based on the modified Eberwine protocol (Eberwine et al. 1992). In brief, 200 ng total RNA was used for cDNA synthesis, followed by an in vitro transcription step for amplification and labeling to synthesize biotin-labelled cRNA using the MessageAmp II RNA amplification kit (Ambion) and biotin-16-UTP (Roche).
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Scanning of the microarray was done by using a Beadstation array scanner; settings were adjusted to a scaling factor of 1 and PMT settings at 430. The data extraction was done for all beads individually and outliers were removed when > 2.5 MAD (median absolute deviation). All remaining data points were used for the calculation of the mean average signal for a given probe and the standard deviation for each probe was calculated.
|
| Description |
biological replicate to sample 4 and 5
Sample 6
|
| Data processing |
The data were normalised using quantile normalisation in R
|
| |
|
| Submission date |
Jun 01, 2015 |
| Last update date |
Oct 28, 2015 |
| Contact name |
Kristin Rattay |
| E-mail(s) |
[email protected]
|
| Organization name |
German Cancer Research Center
|
| Department |
D090
|
| Lab |
Developmental Immunology
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17543 |
| Series (1) |
| GSE69435 |
Genome-wide analysis of TRA (tissue restricted antigen)-specific co-expression groups in mouse medullary thymic epithelial cells (mTECs) |
|
