|
| Status |
Public on Nov 02, 2021 |
| Title |
P09_V1_HDM |
| Sample type |
RNA |
| |
|
| Source name |
CD4+ Tcells
|
| Organism |
Homo sapiens |
| Characteristics |
subjectid: P09
visit: V1
condition: HDM
gender: F
age at visit: 25.19
respiratory symptom score: 38
|
| Treatment protocol |
PBMC from visits V1, V2, and V4 were thawed and cultured together in the presence of HDM extract (0.5mg/ml) or medium control for 24h in Gibco AIM-V medium + 2-Mercaptoethanol (ThermoFisher, Sigma Aldrich), whilst V5 was cultured as a standalone experiment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD4+ T cells were harvested from cultures using positive isolation with Dynabeads (ThermoFisher) and total RNA was extracted with TRIzol followed by RNAeasy.
|
| Label |
biotin
|
| Label protocol |
Total RNA samples (n=198) were labelled according to the manufacturers instructions at the core facility.
|
| |
|
| Hybridization protocol |
Hybridisation was carried at the core facility according to the manufacturers instructions.
|
| Scan protocol |
cDNA was hybridised to Affymetrix PrimeView.
|
| Data processing |
The raw expression data was analysed in the R statistical programming language version 3.4.4. The robust multi-array average (RMA) algorithm was used for background correction, log2 transformation and quantile normalisation. A custom chip description file (primeviewhsentrezgcdf, Version 22) was employed to annotate probe sets to genes based on updated genome and transcriptome information. The data was filtered with the PVAC algorithm and probe sets of low quality were removed. Differentially expressed genes were identified employing moderated t-statistics LIMMA with a false discovery rate (FDR) control for multiple testing.
|
| |
|
| Submission date |
Nov 07, 2018 |
| Last update date |
Nov 02, 2021 |
| Contact name |
Anya Jones |
| E-mail(s) |
[email protected]
|
| Organization name |
Telethon Kids Institute, The University of Western Australia
|
| Lab |
Systems Immunology
|
| Street address |
Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue
|
| City |
Nedlands |
| State/province |
Western Australia |
| ZIP/Postal code |
6009 |
| Country |
Australia |
| |
|
| Platform ID |
GPL25487 |
| Series (1) |
| GSE122290 |
Rewiring of gene networks underlying mite allergen-induced CD4 + Th-cell responses during immunotherapy |
|
