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Series GSE69529 Query DataSets for GSE69529
Status Public on Jun 04, 2015
Title Elucidating the etiology and molecular pathogenicity of infectious diarrhea by high throughput RNA sequencing
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Diarrhea remains a major cause of death in children. Current diagnostic methods largely rely on stool culture and suffer from low sensitivity and inadequate specificity, often leading to inappropriate treatment. The objective of the present study was to use RNA sequencing (RNAseq) analysis to determine blood transcriptional profiles specific for several common pathogenic bacteria and viruses that cause diarrhea in children. We collected whole blood samples from children in Mexico having diarrhea associated with a single pathogen and without systemic complications. Our RNAseq data suggested that the blood signatures can differentiate children with diarrhea from healthy children either with or without bacterial colonization. Moreover, we detected different expression profiles from bacterial and viral infection, demonstrating for the first time the use of RNAseq to identify the etiology of infectious diarrhea.
Overall design 255 whole blood samples from 246 children including children with diarrhea caused by rotavirus (n=60 total; 5 repeated; 55 unique), E.coli (n=55), Salmonella (n=36), Shigella (n=37), adenovirus (n=8), norovirus (n=7), and control children (n=52 total; 4 repeated; 48 unique).
Contributor(s) Khaenam P, Zaidi MJ, Estrada-Gracia T, Popov D, O'Brien K, Nguyen Q, Gersuk V, Presnell S, Eddy J, Linsley PS
Citation(s) 29377961
Submission date Jun 03, 2015
Last update date Jul 29, 2019
Contact name Scott Presnell
Organization name Benaroya Research Institute
Street address 1201 Ninth Avenue
City Seattle
State/province WA
ZIP/Postal code 98101
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (255)
GSM1703026 CT052
GSM1703027 CT016
GSM1703028 CT022
BioProject PRJNA285798
SRA SRP059039

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Supplementary file Size Download File type/resource
GSE69529_GSM2241808-GSM2241855_mexico2_combined_metrics.csv.gz 10.0 Kb (ftp)(http) CSV
GSE69529_GSM2241808-GSM2241855_mexico2_data.csv.gz 1.1 Mb (ftp)(http) CSV
GSE69529_mexico_combined_metrics.csv.gz 39.0 Kb (ftp)(http) CSV
GSE69529_mexico_processed_data_for_GEO.csv.gz 4.9 Mb (ftp)(http) CSV
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Processed data are available on Series record

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