|
| Status |
Public on Nov 01, 2015 |
| Title |
wt CD8 SP thymocytes III |
| Sample type |
RNA |
| |
|
| Source name |
CD8 SP thymocytes
|
| Organism |
Mus musculus |
| Characteristics |
age: 4-6 weeks
strain: C57Bl/6N
genotype/variation: wt
|
| Treatment protocol |
conditional gene knock-out (FoxN1-Cre driven deletion of (Exon3 of) Gpr177/Wls)
|
| Growth protocol |
primary mouse thymocytes isolated from thymi of young adult mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the QIAGEN RNeasy Plus Micro Kit according to the manufactor's instructions. Quality control was performed using the 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 |
replicate 3 CD8 SP wt
|
| Data processing |
data were normalized using quantile normalization in R.
|
| |
|
| Submission date |
Jun 11, 2015 |
| Last update date |
Nov 01, 2015 |
| Contact name |
Fabian Brunk |
| Organization name |
German Cancer Research Center
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17543 |
| Series (1) |
| GSE69766 |
Gene expression profiling of thymocytes from conditional knock-out mice (FoxN1-Cre mediated KO of Gpr177) |
|
