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| 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
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| 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.
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| 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).
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| 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 |
| E-mail(s) |
SPresnell@benaroyaresearch.org
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| Organization name |
Benaroya Research Institute
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| Street address |
1201 Ninth Avenue
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98101 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (255)
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| Relations |
| BioProject |
PRJNA285798 |
| SRA |
SRP059039 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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