Sample Set Annotation Tool: Transcriptional profiling of egg allergy and relationship to disease phenotype - GSE88796

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

To examine the transcriptional response to egg differed between 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, n = 34) and some are baked egg tolerant (BET, n = 20), as well as food allergic controls (AC, n = 14) 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 antigen

Controls

14 non-allergic controls

Methods

PBMCs were isolated from whole blood by Ficoll-Paque PLUS, washed, and cultured in AimV with 2.5% autologous plasma. 4 x 106 cells were plated in 1 ml in 24-well culture plates, in the presence or absence of 300 ug of egg white (EW) protein cleaned of endotoxin using Detoxi-Gel columns.

Additional Information

Expected Samples:

132 Samples Loaded: 132

Species

Human (Homo sapiens)

Sample Source

PBMC

Disease

Allergy

Treatment Protocol

PBMCs were stimulated with egg antigen, gene transcription measured by microarray after 24 hours, and cytokine secretion by multiplex assay after 5 day incubation.

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	batch	treatment	patient	Cytokine measurements availability
GSM2347733	Male	Batch1	Responsive Media	BER1	Yes
GSM2347734	Male	Batch1	Responsive Egg Whites Protein	BER1	Yes
GSM2347735	Male	Batch1	Responsive Media	BER2	Yes
GSM2347736	Male	Batch1	Responsive Egg Whites Protein	BER2	Yes
GSM2347737	Male	Batch1	Responsive Media	BER3	Yes

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File
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	Batch	Treatment	Patient	Cytokine measurements availability	Egg Allergy
GSM2347733	Male	Batch1	Responsive Media	BER1	Yes	Responsive
GSM2347734	Male	Batch1	Responsive Egg Whites Protein	BER1	Yes	Responsive
GSM2347735	Male	Batch1	Responsive Media	BER2	Yes	Responsive
GSM2347736	Male	Batch1	Responsive Egg Whites Protein	BER2	Yes	Responsive
GSM2347737	Male	Batch1	Responsive Media	BER3	Yes	Responsive
GSM2347738	Male	Batch1	Responsive Egg Whites Protein	BER3	Yes	Responsive
GSM2347739	Male	Batch1	Responsive Media	BER4	Yes	Responsive
GSM2347740	Male	Batch1	Responsive Egg Whites Protein	BER4	Yes	Responsive
GSM2347741	Male	Batch1	Responsive Media	BER5	Yes	Responsive
GSM2347742	Male	Batch1	Responsive Egg Whites Protein	BER5	Yes	Responsive
GSM2347743	Male	Batch1	Responsive Media	BER6	Yes	Responsive
GSM2347744	Male	Batch1	Responsive Egg Whites Protein	BER6	Yes	Responsive
GSM2347745	Male	Batch1	Responsive Media	BER7	Yes	Responsive
GSM2347746	Male	Batch1	Responsive Egg Whites Protein	BER7	Yes	Responsive
GSM2347747	Male	Batch1	Responsive Media	BER8	Yes	Responsive
GSM2347748	Male	Batch1	Responsive Egg Whites Protein	BER8	Yes	Responsive
GSM2347749	Male	Batch1	Responsive Egg Whites Protein	BER9	Yes	Responsive
GSM2347750	Male	Batch1	Responsive Media	BER10	No	Responsive
GSM2347751	Male	Batch1	Responsive Egg Whites Protein	BER10	Yes	Responsive
GSM2347752	Female	Batch1	Responsive Media	BER11	No	Responsive
GSM2347753	Female	Batch1	Responsive Egg Whites Protein	BER11	Yes	Responsive
GSM2347754	Male	Batch1	Responsive Media	BER12	Yes	Responsive
GSM2347755	Male	Batch1	Responsive Egg Whites Protein	BER12	Yes	Responsive
GSM2347756	Male	Batch1	Tolerant Media	BET1	Yes	Tolerant
GSM2347757	Male	Batch1	Tolerant Egg Whites Protein	BET1	Yes	Tolerant
GSM2347758	Female	Batch1	Responsive Media	BER13	Yes	Responsive
GSM2347759	Female	Batch1	Responsive Egg Whites Protein	BER13	Yes	Responsive
GSM2347760	Female	Batch1	Responsive Media	BER14	Yes	Responsive
GSM2347761	Female	Batch1	Responsive Egg Whites Protein	BER14	Yes	Responsive
GSM2347762	Male	Batch1	Tolerant Media	BET2	Yes	Tolerant
GSM2347763	Male	Batch1	Tolerant Egg Whites Protein	BET2	Yes	Tolerant
GSM2347764	Male	Batch1	Responsive Media	BER15	Yes	Responsive
GSM2347765	Male	Batch1	Responsive Egg Whites Protein	BER15	Yes	Responsive
GSM2347766	Male	Batch1	Responsive Media	BER16	Yes	Responsive
GSM2347767	Male	Batch1	Responsive Egg Whites Protein	BER16	Yes	Responsive
GSM2347768	Female	Batch1	Tolerant Media	BET3	Yes	Tolerant
GSM2347769	Female	Batch1	Tolerant Egg Whites Protein	BET3	Yes	Tolerant
GSM2347770	Male	Batch2	Non Egg Allergic Media	AC1	Yes	Non Allergic
GSM2347771	Male	Batch2	Non Egg Allergic Egg Whites Protein	AC2	Yes	Non Allergic
GSM2347772	Female	Batch2	Non Egg Allergic Media	AC3	Yes	Non Allergic
GSM2347773	Male	Batch2	Tolerant Egg Whites Protein	BET4	No	Tolerant
GSM2347774	Female	Batch2	Responsive Egg Whites Protein	BER17	Yes	Responsive
GSM2347775	Female	Batch2	Non Egg Allergic Egg Whites Protein	AC4	Yes	Non Allergic
GSM2347776	Male	Batch2	Non Egg Allergic Media	AC5	Yes	Non Allergic
GSM2347777	Male	Batch2	Non Egg Allergic Egg Whites Protein	AC5	Yes	Non Allergic
GSM2347778	Female	Batch2	Responsive Media	BER18	Yes	Responsive
GSM2347779	Female	Batch2	Responsive Egg Whites Protein	BER18	Yes	Responsive
GSM2347780	Male	Batch2	Responsive Media	BER19	No	Responsive
GSM2347781	Male	Batch2	Responsive Egg Whites Protein	BER19	No	Responsive
GSM2347782	Female	Batch2	Responsive Media	BER20	No	Responsive
GSM2347783	Female	Batch2	Responsive Egg Whites Protein	BER20	No	Responsive
GSM2347784	Female	Batch2	Responsive Media	BER21	Yes	Responsive
GSM2347785	Female	Batch2	Responsive Egg Whites Protein	BER21	Yes	Responsive
GSM2347786	Male	Batch2	Responsive Egg Whites Protein	BER22	Yes	Responsive
GSM2347787	Male	Batch2	Responsive Media	BER23	No	Responsive
GSM2347788	Male	Batch2	Responsive Media	BER24	No	Responsive
GSM2347789	Male	Batch2	Responsive Egg Whites Protein	BER24	No	Responsive
GSM2347790	Male	Batch2	Responsive Egg Whites Protein	BER25	No	Responsive
GSM2347791	Female	Batch3	Responsive Media	BER17	Yes	Responsive
GSM2347792	Male	Batch3	Tolerant Media	BET4	No	Tolerant
GSM2347793	Male	Batch3	Non Egg Allergic Media	AC6	Yes	Non Allergic
GSM2347794	Male	Batch3	Non Egg Allergic Media	AC2	Yes	Non Allergic
GSM2347795	Male	Batch3	Non Egg Allergic Egg Whites Protein	AC1	Yes	Non Allergic
GSM2347796	Female	Batch3	Non Egg Allergic Egg Whites Protein	AC3	Yes	Non Allergic
GSM2347797	Male	Batch3	Non Egg Allergic Egg Whites Protein	AC7	Yes	Non Allergic
GSM2347798	Female	Batch3	Responsive Egg Whites Protein	BER26	Yes	Responsive
GSM2347799	Male	Batch3	Responsive Egg Whites Protein	BER27	Yes	Responsive
GSM2347800	Female	Batch4	Responsive Egg Whites Protein	BER28	Yes	Responsive
GSM2347801	Female	Batch4	Responsive Media	BER28	Yes	Responsive
GSM2347802	Male	Batch4	Tolerant Egg Whites Protein	BET5	No	Tolerant
GSM2347803	Male	Batch4	Tolerant Media	BET5	No	Tolerant
GSM2347804	Male	Batch4	Tolerant Egg Whites Protein	BET6	Yes	Tolerant
GSM2347805	Male	Batch4	Tolerant Media	BET6	Yes	Tolerant
GSM2347806	Female	Batch4	Responsive Media	BER26	No	Responsive
GSM2347807	Male	Batch4	Non Egg Allergic Media	AC8	Yes	Non Allergic
GSM2347808	Female	Batch4	Tolerant Egg Whites Protein	BET7	Yes	Tolerant
GSM2347809	Female	Batch4	Tolerant Media	BET7	Yes	Tolerant
GSM2347810	Male	Batch4	Responsive Media	BER29	No	Responsive
GSM2347811	Male	Batch4	Responsive Egg Whites Protein	BER29	No	Responsive
GSM2347812	Male	Batch4	Non Egg Allergic Egg Whites Protein	AC8	Yes	Non Allergic
GSM2347813	Female	Batch4	Tolerant Egg Whites Protein	BET8	Yes	Tolerant
GSM2347814	Male	Batch4	Tolerant Egg Whites Protein	BET9	Yes	Tolerant
GSM2347815	Female	Batch4	Tolerant Egg Whites Protein	BET10	Yes	Tolerant
GSM2347816	Female	Batch4	Tolerant Media	BET10	Yes	Tolerant
GSM2347817	Male	Batch4	Responsive Egg Whites Protein	BER30	Yes	Responsive
GSM2347818	Male	Batch4	Responsive Media	BER30	Yes	Responsive
GSM2347819	Male	Batch4	Tolerant Media	BET9	Yes	Tolerant
GSM2347820	Male	Batch4	Responsive Media	BER27	Yes	Responsive
GSM2347821	Female	Batch4	Responsive Media	BER31	Yes	Responsive
GSM2347822	Female	Batch4	Non Egg Allergic Media	AC4	Yes	Non Allergic
GSM2347823	Male	Batch4	Tolerant Egg Whites Protein	BET11	Yes	Tolerant
GSM2347824	Female	Batch4	Non Egg Allergic Media	AC9	Yes	Non Allergic
GSM2347825	Female	Batch4	Non Egg Allergic Egg Whites Protein	AC9	Yes	Non Allergic
GSM2347826	Female	Batch4	Responsive Egg Whites Protein	BER32	Yes	Responsive
GSM2347827	Female	Batch4	Responsive Media	BER32	Yes	Responsive
GSM2347828	Female	Batch4	Non Egg Allergic Egg Whites Protein	AC10	Yes	Non Allergic
GSM2347829	Female	Batch4	Non Egg Allergic Media	AC10	Yes	Non Allergic
GSM2347830	Male	Batch4	Non Egg Allergic Egg Whites Protein	AC6	Yes	Non Allergic
GSM2347831	Male	Batch4	Non Egg Allergic Media	AC11	Yes	Non Allergic
GSM2347832	Male	Batch4	Non Egg Allergic Egg Whites Protein	AC11	Yes	Non Allergic
GSM2347833	Male	Batch4	Non Egg Allergic Media	AC7	Yes	Non Allergic
GSM2347834	Female	Batch4	Non Egg Allergic Egg Whites Protein	AC12	Yes	Non Allergic
GSM2347835	Female	Batch4	Non Egg Allergic Media	AC12	Yes	Non Allergic
GSM2347836	Female	Batch4	Tolerant Media	BET8	Yes	Tolerant
GSM2347837	Female	Batch4	Responsive Egg Whites Protein	BER31	Yes	Responsive
GSM2347838	Male	Batch4	Responsive Media	BER22	Yes	Responsive
GSM2347839	Male	Batch4	Responsive Egg Whites Protein	BER23	No	Responsive
GSM2347840	Male	Batch5	Tolerant Media	BET12	No	Tolerant
GSM2347841	Male	Batch5	Tolerant Egg Whites Protein	BET12	No	Tolerant
GSM2347842	Male	Batch5	Tolerant Media	BET13	No	Tolerant
GSM2347843	Male	Batch5	Tolerant Egg Whites Protein	BET13	No	Tolerant
GSM2347844	Female	Batch5	Tolerant Media	BET14	Yes	Tolerant
GSM2347845	Female	Batch5	Tolerant Egg Whites Protein	BET14	Yes	Tolerant
GSM2347846	Female	Batch5	Tolerant Media	BET15	Yes	Tolerant
GSM2347847	Female	Batch5	Tolerant Egg Whites Protein	BET15	Yes	Tolerant
GSM2347848	Male	Batch5	Tolerant Media	BET16	No	Tolerant
GSM2347849	Male	Batch5	Tolerant Egg Whites Protein	BET16	No	Tolerant
GSM2347850	Male	Batch5	Tolerant Media	BET17	Yes	Tolerant
GSM2347851	Male	Batch5	Tolerant Egg Whites Protein	BET17	Yes	Tolerant
GSM2347852	Female	Batch5	Responsive Egg Whites Protein	BER33	Yes	Responsive
GSM2347853	Female	Batch5	Non Egg Allergic Media	AC13	Yes	Non Allergic
GSM2347854	Female	Batch5	Non Egg Allergic Egg Whites Protein	AC13	Yes	Non Allergic
GSM2347855	Female	Batch5	Tolerant Media	BET18	Yes	Tolerant
GSM2347856	Female	Batch5	Tolerant Egg Whites Protein	BET18	Yes	Tolerant
GSM2347857	Male	Batch5	Responsive Media	BER34	Yes	Responsive
GSM2347858	Male	Batch5	Responsive Egg Whites Protein	BER34	Yes	Responsive
GSM2347859	Female	Batch5	Tolerant Media	BET19	No	Tolerant
GSM2347860	Female	Batch5	Tolerant Egg Whites Protein	BET19	No	Tolerant
GSM2347861	Male	Batch5	Tolerant Media	BET20	No	Tolerant
GSM2347862	Male	Batch5	Tolerant Egg Whites Protein	BET20	No	Tolerant
GSM2347863	Female	Batch5	Non Egg Allergic Media	AC14	Yes	Non Allergic
GSM2347864	Female	Batch5	Non Egg Allergic Egg Whites Protein	AC14	Yes	Non Allergic

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