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Status |
Public on Sep 02, 2024 |
Title |
Blood_Death_early_Patient-a131 |
Sample type |
RNA |
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Source name |
Blood
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Organism |
Homo sapiens |
Characteristics |
tissue: Blood outcome: Death day: 12 patient_timing: early
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Extracted molecule |
total RNA |
Extraction protocol |
Peripheral blood (2 ml) was collected from each patient, preserved in PAXgene Blood RNA Tubes (QIAGEN) and stored at -80°C until use. Total RNA was extracted using a PAXgene Blood RNA Kit (QIAGEN).
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Label |
biotin
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Label protocol |
Transcriptomic data generation was performed by Gene Tech (Shanghai) using a Affymetrix GeneChip Human Gene 2.0 ST Array according to manufacturer instructions.
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Hybridization protocol |
Transcriptomic data generation was performed by Gene Tech (Shanghai) using a Affymetrix GeneChip Human Gene 2.0 ST Array according to manufacturer instructions.
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Scan protocol |
Transcriptomic data generation was performed by Gene Tech (Shanghai) using a Affymetrix GeneChip Human Gene 2.0 ST Array according to manufacturer instructions.
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Description |
Gene expression data from blood of patient a131 (Death outcome) collected at day 12 (earlytimepoint)
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Data processing |
All analyses used the R statistical programming environment (v3.03). Raw CEL intensity files underwent ‘Perfect Match’ probe set-level normalization including background correction using robust multiarray averaging (RMA), quantile normalization and summarization of gene expression using the median published algorithm (Irizarry et al., 2003). Probe set intensity distributions between arrays (before and after normalization) and MA plots of the log intensity ratio versus the average log intensity were assessed for excessive technical variability. The early phase sample from patient a20 was excluded from analysis as the interquartile range of the expression deviation was substantially outside that exhibited by all other samples. Unexpressed probe sets, exhibiting less fluorescence than background probes and w a PSDABG P value > 0.05 were removed from subsequent analyses.
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Submission date |
May 24, 2024 |
Last update date |
Sep 02, 2024 |
Contact name |
Jeremy Chase Crawford |
E-mail(s) |
jeremy.crawford@stjude.org
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Organization name |
St. Jude Children's Research Hospital
|
Department |
Department of Host-Microbe Interactions
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Street address |
MS 221, 262 Danny Thomas Place
|
City |
Memphis |
State/province |
TN |
ZIP/Postal code |
38105-3678 |
Country |
USA |
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Platform ID |
GPL16686 |
Series (1) |
GSE268303 |
High expression of oleoyl-ACP-hydrolase predicts mortality in patients hospitalized with avian A(H7N9) influenza |
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