|
| Status |
Public on Jul 13, 2018 |
| Title |
PIK3CD patient 1 CD40L |
| Sample type |
RNA |
| |
|
| Source name |
transitional B cells from PIK3CD GOF patients
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: transitional B cells
diagnosis: PIK3CD GOF (APDS)
|
| Treatment protocol |
B cells were stimulated with recombinant CD40 ligand alone or together with IL-21 (50 ng/mL)
|
| Growth protocol |
Human transitional B cells were cultured in RPMI1640 containing 10% FCS for 4 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
1 ng of total RNA was used as input for the amplification and labelling of samples using the Affymetrix WT Pico Kit
|
| |
|
| Hybridization protocol |
3 µg fragmented, biotin labelled ss-cDNA was hybridised to Affymetrix Human Gene Array version 2.1ST. Samples were hybridised to arrays for 16 hours at 45°C in the Affymetrix GeneTitan Instrument
|
| Scan protocol |
Arrays were washed and scanned on the Affymetrix GeneTitanand Affymetrix GC3000 scanner instrument as per manufacturers protocol
|
| Description |
RNA from PIK3CD GOF transitional B cells stimulated with CD40L
|
| Data processing |
Bioconductor packages implemented in the R statistical computing environment, version 3.4.1. The file normalized_data_with_all_control_probesets.txt contains the log2 RMA data for all probe sets including control probe sets. The sample data tables include a subset of the control probe sets found on platform GPL23159.
|
| |
|
| Submission date |
Jul 12, 2018 |
| Last update date |
Jul 13, 2018 |
| Contact name |
Stuart Tangye |
| E-mail(s) |
s.tangye@garvan.org.au
|
| Phone |
+61 2 9295 8455
|
| Organization name |
Garvan Institute of Medical Research
|
| Department |
Immunology
|
| Street address |
384 Victoria St
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL23159 |
| Series (1) |
| GSE116999 |
Identification of differentially expressed genes between control and PIK3CD GOF human activated transitional B cells |
|
