|
| Status |
Public on May 12, 2009 |
| Title |
Sklero_4_v1 |
| Sample type |
RNA |
| |
|
| Source name |
whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: whole blood
disease state: scleroderma
|
| Treatment protocol |
CD4+ CD127low CD25+ (Treg) and CD4+ CD127+ CD25- (Tconv) T cells were stained with CD4, CD25 and CD127 mAb (all from BD Pharmingen) and sorted on a FACSDiva cell sorter. Cell purity after isolation was assessed by intracellular staining for FOXP3 (e-bioscience) and routinely showed purities >95%.
|
| Growth protocol |
Blood samples from patients with systemic sclerosis or bacteremia, respectively, were collected in PAXgene blood RNA tubes (BD Biosciences, Heidelberg, Germany)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from Treg and Tconv cells lysed in TRIzol (Invitrogen, Karlsruhe, Germany) was isolated according to the manufacturer´s protocol with subsequent column purification using the RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany). Total RNA from PAXgene samples was prepared according to the manufacturer´s recommendations including an optional DNAse digestion step.
|
| Label |
biotin
|
| Label protocol |
cDNA and biotin-labeled cRNA synthesis was generated from 100 ng total RNA using the Illumina® TotalPrep™ RNA Amplification Kit (Applied Biosystems, Darmstadt, Germany).
|
| |
|
| Hybridization protocol |
cRNA (1.5 µg) was hybridized to Human-6 Expression BeadChips V1 and V2 (Illumina, San Diego, CA), the standard Illumina hybridization protocol
|
| Scan protocol |
Arrays were scanned on Illumina BeadStation 500x using the standard Illumina scanning protocol
|
| Description |
whole blood from sclerodermma patient
|
| Data processing |
The data were normalised using quantile normalisation in R
|
| |
|
| Submission date |
May 08, 2009 |
| Last update date |
Dec 19, 2012 |
| Contact name |
Joachim Schultze |
| E-mail(s) |
j.schultze@uni-bonn.de
|
| Organization name |
LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)
|
| Department |
Genomics and Immunoregulation
|
| Street address |
Carl-Troll-Strasse 31
|
| City |
Bonn |
| State/province |
NRW |
| ZIP/Postal code |
53115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6097 |
| Series (1) |
| GSE16031 |
A comparison of Illumina bead chips reveals unexpected challenges in the use of newest generation microarrays |
|
