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Sample GSM7873123 Query DataSets for GSM7873123
Status Public on Jan 03, 2024
Title Healthy [A4398_437]
Sample type RNA
 
Source name whole blood
Organism Homo sapiens
Characteristics tissue: whole blood
gender / sex: Female
age in days: 317
age group: Above_six_months
visit: Healthy
disease classification at rsv visit based on resvinet score: 1 - Healthy controls
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 2.513359849
AFFX-BkGr-GC04_st 2.520984404
AFFX-BkGr-GC05_st 2.497332235
AFFX-BkGr-GC06_st 2.481699573
AFFX-BkGr-GC07_st 2.608432249
AFFX-BkGr-GC08_st 2.568512138
AFFX-BkGr-GC09_st 2.6418373
AFFX-BkGr-GC10_st 2.600987443
AFFX-BkGr-GC11_st 2.637229014
AFFX-BkGr-GC12_st 2.858658261
AFFX-BkGr-GC13_st 2.746171324
AFFX-BkGr-GC14_st 2.839783904
AFFX-BkGr-GC15_st 2.976059251
AFFX-BkGr-GC16_st 3.134807961
AFFX-BkGr-GC17_st 3.762879623
AFFX-BkGr-GC18_st 3.862935412
AFFX-BkGr-GC19_st 3.917862939
AFFX-BkGr-GC20_st 4.922219195
AFFX-BkGr-GC21_st 5.070243266
AFFX-BkGr-GC22_st 6.414662612

Total number of rows: 22593

Table truncated, full table size 673 Kbytes.




Supplementary file Size Download File type/resource
GSM7873123_A4398_437.CEL.gz 405.6 Kb (ftp)(http) CEL

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