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Sample GSM7873236 Query DataSets for GSM7873236
Status Public on Jan 03, 2024
Title RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_184]
Sample type RNA
 
Source name whole blood
Organism Homo sapiens
Characteristics tissue: whole blood
gender / sex: Female
age in days: 21
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

Data table header descriptions
ID_REF
VALUE batch corrected

Data table
ID_REF VALUE
AFFX-BkGr-GC03_st 2.58985752
AFFX-BkGr-GC04_st 2.608012711
AFFX-BkGr-GC05_st 2.589356536
AFFX-BkGr-GC06_st 2.557981215
AFFX-BkGr-GC07_st 2.733523291
AFFX-BkGr-GC08_st 2.770435951
AFFX-BkGr-GC09_st 2.812272485
AFFX-BkGr-GC10_st 2.782921472
AFFX-BkGr-GC11_st 2.783027894
AFFX-BkGr-GC12_st 2.980475357
AFFX-BkGr-GC13_st 2.927930898
AFFX-BkGr-GC14_st 3.05101656
AFFX-BkGr-GC15_st 3.097277825
AFFX-BkGr-GC16_st 3.234929829
AFFX-BkGr-GC17_st 3.917510088
AFFX-BkGr-GC18_st 4.040595284
AFFX-BkGr-GC19_st 3.885800959
AFFX-BkGr-GC20_st 4.78614819
AFFX-BkGr-GC21_st 4.892893119
AFFX-BkGr-GC22_st 6.226445483

Total number of rows: 22593

Table truncated, full table size 673 Kbytes.




Supplementary file Size Download File type/resource
GSM7873236_A4398_184.CEL.gz 407.8 Kb (ftp)(http) CEL

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