|
| Status |
Public on Jan 03, 2024 |
| Title |
RSV convalescence, comorbidity [A4398_484] |
| Sample type |
RNA |
| |
|
| Source name |
whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: whole blood
gender / sex: Female
age in days: 22
age group: Below_three_months
visit: RSV convalescence visit
disease classification at rsv visit based on resvinet score: 4 - Severe
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The whole blood samples were collected in Paxgene tubes (PAXgene® Blood RNA Tube, BD) and stored at –80 °C until the processing. The RNA was extracted using QIAsymphony PAXgene Blood RNA Kit (QIAGEN) according to the manufacturer’s instructions. After the quality control, the RNA was further processed for Clariom™ GOScreen microarray (Thermo Fisher).
|
| Label |
biotin
|
| Label protocol |
First strand cDNA was synthesized with a combination of a Poly-dT and random primers containing a 5′-adaptor sequence. A 3’-adaptor was added to the single stranded cDNA followed by low-cycle PCR amplification. The cDNA was used as a template for in vitro transcription (IVT) that produces amplified amounts of antisense mRNA, (cRNA). The cRNA was then used as input for a second round of cDNA synthesis, producing double stranded cDNA.
|
| |
|
| Hybridization protocol |
After fragmentation, denaturation and end-labeling the targets are hybridized on the single GO Screen plate, according to manufacturer’s instructions (Thermo Fisher; GeneChip Pico Reagent Kit).
|
| Scan protocol |
Single sample cartridge arrays were stained on a GeneChip Fluidics Station 450 and scanned on a GeneChip scanner 3000 7G while array plates were stained and imaged on the GeneTitan Multi-Channel Instrument.
|
| Description |
Gene expression data of infants from RESCEU case-control cohort
|
| Data processing |
Microarray data were preprocessed using R, Bioconductor package 40,41. Robust Multi-Array Average (RMA) function was used to normalize the raw data 42. Outliers were removed from the downstream data analysis based on visual guidance on principal component (PC) spectral map and sample clustering (Pearson correlation with complete linkage).
The clinical data necessary for batch correction (site of sample collection) is accessible by request only from the submitting party.
|
| |
|
| Submission date |
Oct 31, 2023 |
| Last update date |
Jan 03, 2024 |
| Contact name |
Deniz Oner |
| E-mail(s) |
deniz.oner@kuleuven.be
|
| Organization name |
KU Leuven
|
| Street address |
Gaston Geenslaan
|
| City |
Leuven |
| ZIP/Postal code |
3001 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL31262 |
| Series (1) |
| GSE246622 |
Single-cell immune profiling reveals markers of emergency myelopoiesis that distinguish severe from mild respiratory syncytial virus (RSV) disease in infants |
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