NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7873156 Query DataSets for GSM7873156
Status Public on Jan 03, 2024
Title RSV convalescence visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_022rr]
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: 2 - Mild
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

Data table header descriptions
ID_REF
VALUE batch corrected

Data table
ID_REF VALUE
AFFX-BkGr-GC03_st 2.650236075
AFFX-BkGr-GC04_st 2.646385977
AFFX-BkGr-GC05_st 2.693020975
AFFX-BkGr-GC06_st 2.585877846
AFFX-BkGr-GC07_st 2.744704072
AFFX-BkGr-GC08_st 2.747003165
AFFX-BkGr-GC09_st 2.758212371
AFFX-BkGr-GC10_st 2.788129377
AFFX-BkGr-GC11_st 2.78714911
AFFX-BkGr-GC12_st 2.952903555
AFFX-BkGr-GC13_st 2.92446592
AFFX-BkGr-GC14_st 2.997423751
AFFX-BkGr-GC15_st 3.074438144
AFFX-BkGr-GC16_st 3.284397042
AFFX-BkGr-GC17_st 3.877588873
AFFX-BkGr-GC18_st 4.106281034
AFFX-BkGr-GC19_st 4.117361742
AFFX-BkGr-GC20_st 5.219861153
AFFX-BkGr-GC21_st 5.453402078
AFFX-BkGr-GC22_st 6.710695118

Total number of rows: 22593

Table truncated, full table size 673 Kbytes.




Supplementary file Size Download File type/resource
GSM7873156_A4398_022rr.CEL.gz 379.6 Kb (ftp)(http) CEL

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap