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Sample GSM7873233 Query DataSets for GSM7873233
Status Public on Jan 03, 2024
Title RSV convalescence visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_071]
Sample type RNA
 
Source name whole blood
Organism Homo sapiens
Characteristics tissue: whole blood
gender / sex: Female
age in days: 182
age group: Above_six_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 2.553239002
AFFX-BkGr-GC04_st 2.656148467
AFFX-BkGr-GC05_st 2.61773114
AFFX-BkGr-GC06_st 2.620677966
AFFX-BkGr-GC07_st 2.747278896
AFFX-BkGr-GC08_st 2.719246896
AFFX-BkGr-GC09_st 2.716079896
AFFX-BkGr-GC10_st 2.775660389
AFFX-BkGr-GC11_st 2.723925264
AFFX-BkGr-GC12_st 2.914129289
AFFX-BkGr-GC13_st 2.932161397
AFFX-BkGr-GC14_st 2.998029347
AFFX-BkGr-GC15_st 3.032067979
AFFX-BkGr-GC16_st 3.247535497
AFFX-BkGr-GC17_st 3.872547133
AFFX-BkGr-GC18_st 3.985069766
AFFX-BkGr-GC19_st 3.968727539
AFFX-BkGr-GC20_st 5.003733122
AFFX-BkGr-GC21_st 5.112246213
AFFX-BkGr-GC22_st 6.555599587

Total number of rows: 22593

Table truncated, full table size 673 Kbytes.




Supplementary file Size Download File type/resource
GSM7873233_A4398_071.CEL.gz 395.4 Kb (ftp)(http) CEL

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