Sample Set Annotation Tool: Diagnosis of childhood bacterial and viral infection using host RNA expression - validation set - GSE72829-GPL6947 [Bacterial Infection, Viral Infection]

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

Genome-wide analysis of transcriptional profiles in children <17 years of age with bacterial or viral infections or with clinical features suggestive of infection. This series is also deposited as (GSE72810).

Hypothesis

Experimental Design

Patients were recruited at or after presentation to hospital. Main inclusion criteria were presence of illness of sufficient severity to warrant blood tests for clinical reasons, in child aged <17 years. Blood was collected into PAX gene tubes (PreAnalytiX). Total RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Labeled cRNA was hybridized to Illumina Human HT-12 V3 Beadchips (Validation set). Numbers of arrays analysed in the validation set were as follows: Definite Bacterial infection (n=23), Definite Viral infection (n=28), Probable Bacterial infection (n=17), Probable Viral infection (n=7), infections of uncertain bacterial or viral aetiology (n=55), Healthy controls (n=16).

Experimental Variables

Bacterial infection (2021 ICD-10-CM code* = A49.9)

Viral infection (2021 ICD-10-CM code* = B99.9)

Controls

Methods

The data were normalised using RSN, after background subtraction and filtering for transcripts common to Illumina HT12-V4The software used for data normalization was 'R' Language and Environment for Statistical Computing (R) 3.1.2

Additional Information

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72829

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72810

Expected Samples:

146 Samples Loaded: 146

Species

Human (Homo sapiens)

Sample Source

Whole Blood

Disease

Bacterial and Viral infection

Treatment Protocol

Growth Protocol

Extraction Protocol

Standard PAXgene blood RNA extraction kit protocol (Qiagen). Label

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	Gender	!Sample_title	tissue	dataset	category
GSM1872657	Male	Definite Bacterial_01 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872658	Female	Definite Bacterial_02 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872659	Male	Definite Bacterial_03 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872660	Female	Definite Bacterial_04 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872661	Female	Definite Bacterial_05 [validation]	Whole Blood	Validation	Definite Bacterial

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File

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Sample ID	Gender	!Sample Title	Tissue	Dataset	Category
GSM1872657	Male	Definite Bacterial_01 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872658	Female	Definite Bacterial_02 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872659	Male	Definite Bacterial_03 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872660	Female	Definite Bacterial_04 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872661	Female	Definite Bacterial_05 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872662	Male	Definite Bacterial_06 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872663	Female	Definite Bacterial_07 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872664	Female	Definite Bacterial_08 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872665	Female	Definite Bacterial_09 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872666	Female	Definite Bacterial_10 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872667	Female	Definite Bacterial_11 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872668	Male	Definite Bacterial_12 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872669	Male	Definite Bacterial_13 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872670	Female	Definite Bacterial_14 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872671	Female	Definite Bacterial_15 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872672	Male	Definite Bacterial_16 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872673	Male	Definite Bacterial_17 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872674	Female	Definite Bacterial_18 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872675	Male	Definite Bacterial_19 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872676	Female	Definite Bacterial_20 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872677	Male	Definite Bacterial_21 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872678	Female	Definite Bacterial_22 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872679	Male	Definite Bacterial_23 [validation]	Whole Blood	Validation	Definite Bacterial
GSM1872680	Male	Definite Viral_01 [validation]	Whole Blood	Validation	Definite Viral
GSM1872681	Male	Definite Viral_02 [validation]	Whole Blood	Validation	Definite Viral
GSM1872682	Male	Definite Viral_03 [validation]	Whole Blood	Validation	Definite Viral
GSM1872683	Female	Definite Viral_04 [validation]	Whole Blood	Validation	Definite Viral
GSM1872684	Male	Definite Viral_05 [validation]	Whole Blood	Validation	Definite Viral
GSM1872685	Female	Definite Viral_06 [validation]	Whole Blood	Validation	Definite Viral
GSM1872686	Male	Definite Viral_07 [validation]	Whole Blood	Validation	Definite Viral
GSM1872687	Female	Definite Viral_08 [validation]	Whole Blood	Validation	Definite Viral
GSM1872688	Female	Definite Viral_09 [validation]	Whole Blood	Validation	Definite Viral
GSM1872689	Female	Definite Viral_10 [validation]	Whole Blood	Validation	Definite Viral
GSM1872690	Male	Definite Viral_11 [validation]	Whole Blood	Validation	Definite Viral
GSM1872691	Male	Definite Viral_12 [validation]	Whole Blood	Validation	Definite Viral
GSM1872692	Male	Definite Viral_13 [validation]	Whole Blood	Validation	Definite Viral
GSM1872693	Female	Definite Viral_14 [validation]	Whole Blood	Validation	Definite Viral
GSM1872694	Female	Definite Viral_15 [validation]	Whole Blood	Validation	Definite Viral
GSM1872695	Female	Definite Viral_16 [validation]	Whole Blood	Validation	Definite Viral
GSM1872696	Male	Definite Viral_17 [validation]	Whole Blood	Validation	Definite Viral
GSM1872697	Male	Definite Viral_18 [validation]	Whole Blood	Validation	Definite Viral
GSM1872698	Female	Definite Viral_19 [validation]	Whole Blood	Validation	Definite Viral
GSM1872699	Male	Definite Viral_20 [validation]	Whole Blood	Validation	Definite Viral
GSM1872700	Male	Definite Viral_21 [validation]	Whole Blood	Validation	Definite Viral
GSM1872701	Male	Definite Viral_22 [validation]	Whole Blood	Validation	Definite Viral
GSM1872702	Male	Definite Viral_23 [validation]	Whole Blood	Validation	Definite Viral
GSM1872703	Male	Definite Viral_24 [validation]	Whole Blood	Validation	Definite Viral
GSM1872704	Male	Definite Viral_25 [validation]	Whole Blood	Validation	Definite Viral
GSM1872705	Female	Definite Viral_26 [validation]	Whole Blood	Validation	Definite Viral
GSM1872706	Female	Definite Viral_27 [validation]	Whole Blood	Validation	Definite Viral
GSM1872707	Male	Definite Viral_28 [validation]	Whole Blood	Validation	Definite Viral
GSM1872708	Female	Probable Bacterial_01 [validation]	Whole Blood	Validation	Probable Bacterial
GSM1872709	Female	Probable Bacterial_02 [validation]	Whole Blood	Validation	Probable Bacterial
GSM1872710	Female	Probable Bacterial_03 [validation]	Whole Blood	Validation	Probable Bacterial
GSM1872711	Male	Probable Bacterial_04 [validation]	Whole Blood	Validation	Probable Bacterial
GSM1872712	Male	Probable Bacterial_05 [validation]	Whole Blood	Validation	Probable Bacterial
GSM1872713	Female	Probable Bacterial_06 [validation]	Whole Blood	Validation	Probable Bacterial
GSM1872714	Female	Probable Bacterial_07 [validation]	Whole Blood	Validation	Probable Bacterial
GSM1872715	Female	Probable Bacterial_08 [validation]	Whole Blood	Validation	Probable Bacterial
GSM1872716	Male	Probable Bacterial_09 [validation]	Whole Blood	Validation	Probable Bacterial
GSM1872717	Female	Probable Bacterial_10 [validation]	Whole Blood	Validation	Probable Bacterial
GSM1872718	Male	Probable Bacterial_11 [validation]	Whole Blood	Validation	Probable Bacterial
GSM1872719	Female	Probable Bacterial_12 [validation]	Whole Blood	Validation	Probable Bacterial
GSM1872720	Male	Probable Bacterial_13 [validation]	Whole Blood	Validation	Probable Bacterial
GSM1872721	Female	Probable Bacterial_14 [validation]	Whole Blood	Validation	Probable Bacterial
GSM1872722	Female	Probable Bacterial_15 [validation]	Whole Blood	Validation	Probable Bacterial
GSM1872723	Male	Probable Bacterial_16 [validation]	Whole Blood	Validation	Probable Bacterial
GSM1872724	Male	Probable Bacterial_17 [validation]	Whole Blood	Validation	Probable Bacterial
GSM1872725	Male	Probable Viral_01 [validation]	Whole Blood	Validation	Probable Viral
GSM1872726	Female	Probable Viral_02 [validation]	Whole Blood	Validation	Probable Viral
GSM1872727	Male	Probable Viral_03 [validation]	Whole Blood	Validation	Probable Viral
GSM1872728	Female	Probable Viral_04 [validation]	Whole Blood	Validation	Probable Viral
GSM1872729	Female	Probable Viral_05 [validation]	Whole Blood	Validation	Probable Viral
GSM1872730	Male	Probable Viral_06 [validation]	Whole Blood	Validation	Probable Viral
GSM1872731	Male	Probable Viral_07 [validation]	Whole Blood	Validation	Probable Viral
GSM1872732	Male	Unknown_01 [validation]	Whole Blood	Validation	Uncertain
GSM1872733	Male	Unknown_02 [validation]	Whole Blood	Validation	Uncertain
GSM1872734	Male	Unknown_03 [validation]	Whole Blood	Validation	Uncertain
GSM1872735	Female	Unknown_04 [validation]	Whole Blood	Validation	Uncertain
GSM1872736	Male	Unknown_05 [validation]	Whole Blood	Validation	Uncertain
GSM1872737	Male	Unknown_06 [validation]	Whole Blood	Validation	Uncertain
GSM1872738	Female	Unknown_07 [validation]	Whole Blood	Validation	Uncertain
GSM1872739	Male	Unknown_08 [validation]	Whole Blood	Validation	Uncertain
GSM1872740	Female	Unknown_09 [validation]	Whole Blood	Validation	Uncertain
GSM1872741	Male	Unknown_10 [validation]	Whole Blood	Validation	Uncertain
GSM1872742	Male	Unknown_11 [validation]	Whole Blood	Validation	Uncertain
GSM1872743	Male	Unknown_12 [validation]	Whole Blood	Validation	Uncertain
GSM1872744	Male	Unknown_13 [validation]	Whole Blood	Validation	Uncertain
GSM1872745	Male	Unknown_14 [validation]	Whole Blood	Validation	Uncertain
GSM1872746	Male	Unknown_15 [validation]	Whole Blood	Validation	Uncertain
GSM1872747	Male	Unknown_16 [validation]	Whole Blood	Validation	Uncertain
GSM1872748	Male	Unknown_17 [validation]	Whole Blood	Validation	Uncertain
GSM1872749	Female	Unknown_18 [validation]	Whole Blood	Validation	Uncertain
GSM1872750	Male	Unknown_19 [validation]	Whole Blood	Validation	Uncertain
GSM1872751	Male	Unknown_20 [validation]	Whole Blood	Validation	Uncertain
GSM1872752	Male	Unknown_21 [validation]	Whole Blood	Validation	Uncertain
GSM1872753	Female	Unknown_22 [validation]	Whole Blood	Validation	Uncertain
GSM1872754	Male	Unknown_23 [validation]	Whole Blood	Validation	Uncertain
GSM1872755	Female	Unknown_24 [validation]	Whole Blood	Validation	Uncertain
GSM1872756	Male	Unknown_25 [validation]	Whole Blood	Validation	Uncertain
GSM1872757	Male	Unknown_26 [validation]	Whole Blood	Validation	Uncertain
GSM1872758	Female	Unknown_27 [validation]	Whole Blood	Validation	Uncertain
GSM1872759	Female	Unknown_28 [validation]	Whole Blood	Validation	Uncertain
GSM1872760	Male	Unknown_29 [validation]	Whole Blood	Validation	Uncertain
GSM1872761	Male	Unknown_30 [validation]	Whole Blood	Validation	Uncertain
GSM1872762	Female	Unknown_31 [validation]	Whole Blood	Validation	Uncertain
GSM1872763	Female	Unknown_32 [validation]	Whole Blood	Validation	Uncertain
GSM1872764	Male	Unknown_33 [validation]	Whole Blood	Validation	Uncertain
GSM1872765	Male	Unknown_34 [validation]	Whole Blood	Validation	Uncertain
GSM1872766	Male	Unknown_35 [validation]	Whole Blood	Validation	Uncertain
GSM1872767	Female	Unknown_36 [validation]	Whole Blood	Validation	Uncertain
GSM1872768	Male	Unknown_37 [validation]	Whole Blood	Validation	Uncertain
GSM1872769	Female	Unknown_38 [validation]	Whole Blood	Validation	Uncertain
GSM1872770	Female	Unknown_39 [validation]	Whole Blood	Validation	Uncertain
GSM1872771	Male	Unknown_40 [validation]	Whole Blood	Validation	Uncertain
GSM1872772	Female	Unknown_41 [validation]	Whole Blood	Validation	Uncertain
GSM1872773	Female	Unknown_42 [validation]	Whole Blood	Validation	Uncertain
GSM1872774	Male	Unknown_43 [validation]	Whole Blood	Validation	Uncertain
GSM1872775	Female	Unknown_44 [validation]	Whole Blood	Validation	Uncertain
GSM1872776	Female	Unknown_45 [validation]	Whole Blood	Validation	Uncertain
GSM1872777	Male	Unknown_46 [validation]	Whole Blood	Validation	Uncertain
GSM1872778	Male	Unknown_47 [validation]	Whole Blood	Validation	Uncertain
GSM1872779	Male	Unknown_48 [validation]	Whole Blood	Validation	Uncertain
GSM1872780	Male	Unknown_49 [validation]	Whole Blood	Validation	Uncertain
GSM1872781	Male	Unknown_50 [validation]	Whole Blood	Validation	Uncertain
GSM1872782	Male	Unknown_51 [validation]	Whole Blood	Validation	Uncertain
GSM1872783	Female	Unknown_52 [validation]	Whole Blood	Validation	Uncertain
GSM1872784	Male	Unknown_53 [validation]	Whole Blood	Validation	Uncertain
GSM1872785	Male	Unknown_54 [validation]	Whole Blood	Validation	Uncertain
GSM1872786	Female	Unknown_55 [validation]	Whole Blood	Validation	Uncertain
GSM2126114	Male	Control_01 [validation]	whole blood	Validation	Control
GSM2126115	Male	Control_02 [validation]	whole blood	Validation	Control
GSM2126116	Male	Control_03 [validation]	whole blood	Validation	Control
GSM2126117	Male	Control_04 [validation]	whole blood	Validation	Control
GSM2126118	Male	Control_05 [validation]	whole blood	Validation	Control
GSM2126119	Female	Control_06 [validation]	whole blood	Validation	Control
GSM2126120	Female	Control_07 [validation]	whole blood	Validation	Control
GSM2126121	Male	Control_08 [validation]	whole blood	Validation	Control
GSM2126122	Male	Control_09 [validation]	whole blood	Validation	Control
GSM2126123	Male	Control_10 [validation]	whole blood	Validation	Control
GSM2126124	Female	Control_11 [validation]	whole blood	Validation	Control
GSM2126125	Female	Control_12 [validation]	whole blood	Validation	Control
GSM2126126	Female	Control_13 [validation]	whole blood	Validation	Control
GSM2126127	Female	Control_14 [validation]	whole blood	Validation	Control
GSM2126128	Male	Control_15 [validation]	whole blood	Validation	Control
GSM2126129	Male	Control_16 [validation]	whole blood	Validation	Control

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