Sample Set Annotation Tool: Transcriptional profiling of egg allergy and relationship to disease phenotype

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

To characterize the of gene expression of PBMCs from egg allergic and clinically tolerant subjects.

Hypothesis

Experimental Design

PBMCs were obtained from egg allergic children, some of whom are baked egg responsive (BER) and some are baked egg tolerant (BET), as well as food allergic controls (AC) who were clinically tolerant to egg. PBMCs were stimulated with egg antigen, gene transcription measured by microarray after 24 hours, and cytokine secretion by multiplex assay after 5 day incubation.

Experimental Variables

Egg atigen

Controls

Food allergic controls

Methods

Additional Information

In lumi, the data are transformed (variance-stabilizing transformation (VST)) and normalized (robust spline normalization (RSN)), resulting in log-transformed normalized data.

Expected Samples:

132 Samples Loaded: 132

Species

Human (Homo sapiens)

Sample Source

PBMC

Disease

Allergy

Treatment Protocol

hey

Growth Protocol

Extraction Protocol

Media was removed and cells harvested for RNA isolation using the Qiagen RNeasy mini kit according to manufacturer’s instructions.

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	Gender	group	patient	Egg Allergy	Incubation conditions
GSM2347733	Male	Allergic_Control	BER1	Allergic	Control
GSM2347734	Male	Allergic_Egg	BER1	Allergic	Egg
GSM2347735	Male	Allergic_Control	BER2	Allergic	Control
GSM2347736	Male	Allergic_Egg	BER2	Allergic	Egg
GSM2347737	Male	Allergic_Control	BER3	Allergic	Control

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File
GSE88796_v1.csv Sample Set Spreadsheet
GSE88796_v1.csv Sample Set Spreadsheet
GSE88796_v1.csv Sample Set Spreadsheet

Samples Viewer / Editor

All fields are editable except the "Sample ID" column. To edit a cell, click within the cell. To edit a "date" cell, click on the calendar icon. To cancel an edit, press the ESC key.

Sample ID	Gender	Group	Patient	Egg Allergy	Incubation conditions
GSM2347733	Male	Allergic_Control	BER1	Allergic	Control
GSM2347734	Male	Allergic_Egg	BER1	Allergic	Egg
GSM2347735	Male	Allergic_Control	BER2	Allergic	Control
GSM2347736	Male	Allergic_Egg	BER2	Allergic	Egg
GSM2347737	Male	Allergic_Control	BER3	Allergic	Control
GSM2347738	Male	Allergic_Egg	BER3	Allergic	Egg
GSM2347739	Male	Allergic_Control	BER4	Allergic	Control
GSM2347740	Male	Allergic_Egg	BER4	Allergic	Egg
GSM2347741	Male	Allergic_Control	BER5	Allergic	Control
GSM2347742	Male	Allergic_Egg	BER5	Allergic	Egg
GSM2347743	Male	Allergic_Control	BER6	Allergic	Control
GSM2347744	Male	Allergic_Egg	BER6	Allergic	Egg
GSM2347745	Male	Allergic_Control	BER7	Allergic	Control
GSM2347746	Male	Allergic_Egg	BER7	Allergic	Egg
GSM2347747	Male	Allergic_Control	BER8	Allergic	Control
GSM2347748	Male	Allergic_Egg	BER8	Allergic	Egg
GSM2347749	Male	Allergic_Egg	BER9	Allergic	Egg
GSM2347750	Male	Allergic_Control	BER10	Allergic	Control
GSM2347751	Male	Allergic_Egg	BER10	Allergic	Egg
GSM2347752	Female	Allergic_Control	BER11	Allergic	Control
GSM2347753	Female	Allergic_Egg	BER11	Allergic	Egg
GSM2347754	Male	Allergic_Control	BER12	Allergic	Control
GSM2347755	Male	Allergic_Egg	BER12	Allergic	Egg
GSM2347756	Male	Tolerant_Control	BET1	Tolerant	Control
GSM2347757	Male	Tolerant_Egg	BET1	Tolerant	Egg
GSM2347758	Female	Allergic_Control	BER13	Allergic	Control
GSM2347759	Female	Allergic_Egg	BER13	Allergic	Egg
GSM2347760	Female	Allergic_Control	BER14	Allergic	Control
GSM2347761	Female	Allergic_Egg	BER14	Allergic	Egg
GSM2347762	Male	Tolerant_Control	BET2	Tolerant	Control
GSM2347763	Male	Tolerant_Egg	BET2	Tolerant	Egg
GSM2347764	Male	Allergic_Control	BER15	Allergic	Control
GSM2347765	Male	Allergic_Egg	BER15	Allergic	Egg
GSM2347766	Male	Allergic_Control	BER16	Allergic	Control
GSM2347767	Male	Allergic_Egg	BER16	Allergic	Egg
GSM2347768	Female	Tolerant_Control	BET3	Tolerant	Control
GSM2347769	Female	Tolerant_Egg	BET3	Tolerant	Egg
GSM2347770	Male	Healthy_Control	AC1	Healthy	Control
GSM2347771	Male	Healthy_Egg	AC2	Healthy	Egg
GSM2347772	Female	Healthy_Control	AC3	Healthy	Control
GSM2347773	Male	Tolerant_Egg	BET4	Tolerant	Egg
GSM2347774	Female	Allergic_Egg	BER17	Allergic	Egg
GSM2347775	Female	Healthy_Egg	AC4	Healthy	Egg
GSM2347776	Male	Healthy_Control	AC5	Healthy	Control
GSM2347777	Male	Healthy_Egg	AC5	Healthy	Egg
GSM2347778	Female	Allergic_Control	BER18	Allergic	Control
GSM2347779	Female	Allergic_Egg	BER18	Allergic	Egg
GSM2347780	Male	Allergic_Control	BER19	Allergic	Control
GSM2347781	Male	Allergic_Egg	BER19	Allergic	Egg
GSM2347782	Female	Allergic_Control	BER20	Allergic	Control
GSM2347783	Female	Allergic_Egg	BER20	Allergic	Egg
GSM2347784	Female	Allergic_Control	BER21	Allergic	Control
GSM2347785	Female	Allergic_Egg	BER21	Allergic	Egg
GSM2347786	Male	Allergic_Egg	BER22	Allergic	Egg
GSM2347787	Male	Allergic_Control	BER23	Allergic	Control
GSM2347788	Male	Allergic_Control	BER24	Allergic	Control
GSM2347789	Male	Allergic_Egg	BER24	Allergic	Egg
GSM2347790	Male	Allergic_Egg	BER25	Allergic	Egg
GSM2347791	Female	Allergic_Control	BER17	Allergic	Control
GSM2347792	Male	Tolerant_Control	BET4	Tolerant	Control
GSM2347793	Male	Healthy_Control	AC6	Healthy	Control
GSM2347794	Male	Healthy_Control	AC2	Healthy	Control
GSM2347795	Male	Healthy_Egg	AC1	Healthy	Egg
GSM2347796	Female	Healthy_Egg	AC3	Healthy	Egg
GSM2347797	Male	Healthy_Egg	AC7	Healthy	Egg
GSM2347798	Female	Allergic_Egg	BER26	Allergic	Egg
GSM2347799	Male	Allergic_Egg	BER27	Allergic	Egg
GSM2347800	Female	Allergic_Egg	BER28	Allergic	Egg
GSM2347801	Female	Allergic_Control	BER28	Allergic	Control
GSM2347802	Male	Tolerant_Egg	BET5	Tolerant	Egg
GSM2347803	Male	Tolerant_Control	BET5	Tolerant	Control
GSM2347804	Male	Tolerant_Egg	BET6	Tolerant	Egg
GSM2347805	Male	Tolerant_Control	BET6	Tolerant	Control
GSM2347806	Female	Allergic_Control	BER26	Allergic	Control
GSM2347807	Male	Healthy_Control	AC8	Healthy	Control
GSM2347808	Female	Tolerant_Egg	BET7	Tolerant	Egg
GSM2347809	Female	Tolerant_Control	BET7	Tolerant	Control
GSM2347810	Male	Allergic_Control	BER29	Allergic	Control
GSM2347811	Male	Allergic_Egg	BER29	Allergic	Egg
GSM2347812	Male	Healthy_Egg	AC8	Healthy	Egg
GSM2347813	Female	Tolerant_Egg	BET8	Tolerant	Egg
GSM2347814	Male	Tolerant_Egg	BET9	Tolerant	Egg
GSM2347815	Female	Tolerant_Egg	BET10	Tolerant	Egg
GSM2347816	Female	Tolerant_Control	BET10	Tolerant	Control
GSM2347817	Male	Allergic_Egg	BER30	Allergic	Egg
GSM2347818	Male	Allergic_Control	BER30	Allergic	Control
GSM2347819	Male	Tolerant_Control	BET9	Tolerant	Control
GSM2347820	Male	Allergic_Control	BER27	Allergic	Control
GSM2347821	Female	Allergic_Control	BER31	Allergic	Control
GSM2347822	Female	Healthy_Control	AC4	Healthy	Control
GSM2347823	Male	Tolerant_Egg	BET11	Tolerant	Egg
GSM2347824	Female	Healthy_Control	AC9	Healthy	Control
GSM2347825	Female	Healthy_Egg	AC9	Healthy	Egg
GSM2347826	Female	Allergic_Egg	BER32	Allergic	Egg
GSM2347827	Female	Allergic_Control	BER32	Allergic	Control
GSM2347828	Female	Healthy_Egg	AC10	Healthy	Egg
GSM2347829	Female	Healthy_Control	AC10	Healthy	Control
GSM2347830	Male	Healthy_Egg	AC6	Healthy	Egg
GSM2347831	Male	Healthy_Control	AC11	Healthy	Control
GSM2347832	Male	Healthy_Egg	AC11	Healthy	Egg
GSM2347833	Male	Healthy_Control	AC7	Healthy	Control
GSM2347834	Female	Healthy_Egg	AC12	Healthy	Egg
GSM2347835	Female	Healthy_Control	AC12	Healthy	Control
GSM2347836	Female	Tolerant_Control	BET8	Tolerant	Control
GSM2347837	Female	Allergic_Egg	BER31	Allergic	Egg
GSM2347838	Male	Allergic_Control	BER22	Allergic	Control
GSM2347839	Male	Allergic_Egg	BER23	Allergic	Egg
GSM2347840	Male	Tolerant_Control	BET12	Tolerant	Control
GSM2347841	Male	Tolerant_Egg	BET12	Tolerant	Egg
GSM2347842	Male	Tolerant_Control	BET13	Tolerant	Control
GSM2347843	Male	Tolerant_Egg	BET13	Tolerant	Egg
GSM2347844	Female	Tolerant_Control	BET14	Tolerant	Control
GSM2347845	Female	Tolerant_Egg	BET14	Tolerant	Egg
GSM2347846	Female	Tolerant_Control	BET15	Tolerant	Control
GSM2347847	Female	Tolerant_Egg	BET15	Tolerant	Egg
GSM2347848	Male	Tolerant_Control	BET16	Tolerant	Control
GSM2347849	Male	Tolerant_Egg	BET16	Tolerant	Egg
GSM2347850	Male	Tolerant_Control	BET17	Tolerant	Control
GSM2347851	Male	Tolerant_Egg	BET17	Tolerant	Egg
GSM2347852	Female	Allergic_Egg	BER33	Allergic	Egg
GSM2347853	Female	Healthy_Control	AC13	Healthy	Control
GSM2347854	Female	Healthy_Egg	AC13	Healthy	Egg
GSM2347855	Female	Tolerant_Control	BET18	Tolerant	Control
GSM2347856	Female	Tolerant_Egg	BET18	Tolerant	Egg
GSM2347857	Male	Allergic_Control	BER34	Allergic	Control
GSM2347858	Male	Allergic_Egg	BER34	Allergic	Egg
GSM2347859	Female	Tolerant_Control	BET19	Tolerant	Control
GSM2347860	Female	Tolerant_Egg	BET19	Tolerant	Egg
GSM2347861	Male	Tolerant_Control	BET20	Tolerant	Control
GSM2347862	Male	Tolerant_Egg	BET20	Tolerant	Egg
GSM2347863	Female	Healthy_Control	AC14	Healthy	Control
GSM2347864	Female	Healthy_Egg	AC14	Healthy	Egg

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SIDRA