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Sample GSM8289339 Query DataSets for GSM8289339
Status Public on Sep 02, 2024
Title Blood_Death_early_Patient-a131
Sample type RNA
 
Source name Blood
Organism Homo sapiens
Characteristics tissue: Blood
outcome: Death
day: 12
patient_timing: early
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).
Label biotin
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.
 
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.
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.
Description Gene expression data from blood of patient a131 (Death outcome) collected at day 12 (earlytimepoint)
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.
 
Submission date May 24, 2024
Last update date Sep 02, 2024
Contact name Jeremy Chase Crawford
E-mail(s) jeremy.crawford@stjude.org
Organization name St. Jude Children's Research Hospital
Department Department of Host-Microbe Interactions
Street address MS 221, 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38105-3678
Country USA
 
Platform ID GPL16686
Series (1)
GSE268303 High expression of oleoyl-ACP-hydrolase predicts mortality in patients hospitalized with avian A(H7N9) influenza

Data table header descriptions
ID_REF
VALUE normalized log2 intensity

Data table
ID_REF VALUE
16650001 1.460696457
16650003 2.626913634
16650005 1.753104541
16650007 1.900924705
16650009 1.045597702
16650011 1.739716557
16650013 3.383081545
16650015 3.270901375
16650017 3.37670877
16650019 2.738465924
16650021 2.141491362
16650023 1.946501136
16650025 1.449417423
16650027 2.110694569
16650029 2.309347655
16650031 3.812066199
16650033 1.282307246
16650035 0.984055565
16650037 1.519194412
16650041 5.071187524

Total number of rows: 53617

Table truncated, full table size 1093 Kbytes.




Supplementary file Size Download File type/resource
GSM8289339_16_HuGene-2_0-st_.CEL.gz 7.3 Mb (ftp)(http) CEL

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