Optimizing high dimensional gene expression studies for immune response following smallpox vaccination using Taqman® Low density immune arrays

Ann L Oberg, Neelam Dhiman, Diane E. Grill, Jenna E. Ryan, Richard B Kennedy, Gregory A. Poland

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Introduction: We sought to determine the time and vaccinia virus dose combination that would maximize the number of acute immune response changes in response to vaccinia stimulation in preparation for a large gene expression microarray experiment. Methods: PBMCs from ten subjects were exposed to five vaccinia virus doses for three lengths of time. Gene expression was measured for 90 immune response genes via Taqman® Low Density Immune Arrays. Expression data were normalized via model-based non-linear normalization. Linear mixed effects model results were used to standardize changes across genes and determine the time/multiplicity of infection (MOI) combination with the largest number of changes. Results: The greatest number of changes occurred with a MOI of 5.0 and exposure time of 48. h. Further inspection revealed that most changes had occurred earlier and faded at this combination. The second highest number of changes was found at a MOI of 0.5. PFU/cell and time of 18. h. Conclusions: We conclude a time of 18. h with a MOI of 0.5. PFU/cell is the optimal time/MOI combination for the full scale gene expression study. The strategy described herein is a general and resource efficient way to make critical decisions regarding experimental parameters for studies utilizing expensive assays that interrogate a large number of variables.

Original languageEnglish (US)
Pages (from-to)69-78
Number of pages10
JournalJournal of Immunological Methods
Volume366
Issue number1-2
DOIs
StatePublished - Mar 7 2011

Fingerprint

Smallpox
Vaccination
Gene Expression
Infection
Vaccinia virus
Vaccinia
Nonlinear Dynamics
Genes

Keywords

  • Microarray
  • Smallpox
  • TLDA
  • Vaccinia virus

ASJC Scopus subject areas

  • Immunology
  • Immunology and Allergy

Cite this

Optimizing high dimensional gene expression studies for immune response following smallpox vaccination using Taqman® Low density immune arrays. / Oberg, Ann L; Dhiman, Neelam; Grill, Diane E.; Ryan, Jenna E.; Kennedy, Richard B; Poland, Gregory A.

In: Journal of Immunological Methods, Vol. 366, No. 1-2, 07.03.2011, p. 69-78.

Research output: Contribution to journalArticle

@article{7eee33fcb16b4a0fbb417578c1681124,
title = "Optimizing high dimensional gene expression studies for immune response following smallpox vaccination using Taqman{\circledR} Low density immune arrays",
abstract = "Introduction: We sought to determine the time and vaccinia virus dose combination that would maximize the number of acute immune response changes in response to vaccinia stimulation in preparation for a large gene expression microarray experiment. Methods: PBMCs from ten subjects were exposed to five vaccinia virus doses for three lengths of time. Gene expression was measured for 90 immune response genes via Taqman{\circledR} Low Density Immune Arrays. Expression data were normalized via model-based non-linear normalization. Linear mixed effects model results were used to standardize changes across genes and determine the time/multiplicity of infection (MOI) combination with the largest number of changes. Results: The greatest number of changes occurred with a MOI of 5.0 and exposure time of 48. h. Further inspection revealed that most changes had occurred earlier and faded at this combination. The second highest number of changes was found at a MOI of 0.5. PFU/cell and time of 18. h. Conclusions: We conclude a time of 18. h with a MOI of 0.5. PFU/cell is the optimal time/MOI combination for the full scale gene expression study. The strategy described herein is a general and resource efficient way to make critical decisions regarding experimental parameters for studies utilizing expensive assays that interrogate a large number of variables.",
keywords = "Microarray, Smallpox, TLDA, Vaccinia virus",
author = "Oberg, {Ann L} and Neelam Dhiman and Grill, {Diane E.} and Ryan, {Jenna E.} and Kennedy, {Richard B} and Poland, {Gregory A.}",
year = "2011",
month = "3",
day = "7",
doi = "10.1016/j.jim.2011.01.011",
language = "English (US)",
volume = "366",
pages = "69--78",
journal = "Journal of Immunological Methods",
issn = "0022-1759",
publisher = "Elsevier",
number = "1-2",

}

TY - JOUR

T1 - Optimizing high dimensional gene expression studies for immune response following smallpox vaccination using Taqman® Low density immune arrays

AU - Oberg, Ann L

AU - Dhiman, Neelam

AU - Grill, Diane E.

AU - Ryan, Jenna E.

AU - Kennedy, Richard B

AU - Poland, Gregory A.

PY - 2011/3/7

Y1 - 2011/3/7

N2 - Introduction: We sought to determine the time and vaccinia virus dose combination that would maximize the number of acute immune response changes in response to vaccinia stimulation in preparation for a large gene expression microarray experiment. Methods: PBMCs from ten subjects were exposed to five vaccinia virus doses for three lengths of time. Gene expression was measured for 90 immune response genes via Taqman® Low Density Immune Arrays. Expression data were normalized via model-based non-linear normalization. Linear mixed effects model results were used to standardize changes across genes and determine the time/multiplicity of infection (MOI) combination with the largest number of changes. Results: The greatest number of changes occurred with a MOI of 5.0 and exposure time of 48. h. Further inspection revealed that most changes had occurred earlier and faded at this combination. The second highest number of changes was found at a MOI of 0.5. PFU/cell and time of 18. h. Conclusions: We conclude a time of 18. h with a MOI of 0.5. PFU/cell is the optimal time/MOI combination for the full scale gene expression study. The strategy described herein is a general and resource efficient way to make critical decisions regarding experimental parameters for studies utilizing expensive assays that interrogate a large number of variables.

AB - Introduction: We sought to determine the time and vaccinia virus dose combination that would maximize the number of acute immune response changes in response to vaccinia stimulation in preparation for a large gene expression microarray experiment. Methods: PBMCs from ten subjects were exposed to five vaccinia virus doses for three lengths of time. Gene expression was measured for 90 immune response genes via Taqman® Low Density Immune Arrays. Expression data were normalized via model-based non-linear normalization. Linear mixed effects model results were used to standardize changes across genes and determine the time/multiplicity of infection (MOI) combination with the largest number of changes. Results: The greatest number of changes occurred with a MOI of 5.0 and exposure time of 48. h. Further inspection revealed that most changes had occurred earlier and faded at this combination. The second highest number of changes was found at a MOI of 0.5. PFU/cell and time of 18. h. Conclusions: We conclude a time of 18. h with a MOI of 0.5. PFU/cell is the optimal time/MOI combination for the full scale gene expression study. The strategy described herein is a general and resource efficient way to make critical decisions regarding experimental parameters for studies utilizing expensive assays that interrogate a large number of variables.

KW - Microarray

KW - Smallpox

KW - TLDA

KW - Vaccinia virus

UR - http://www.scopus.com/inward/record.url?scp=79952316511&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79952316511&partnerID=8YFLogxK

U2 - 10.1016/j.jim.2011.01.011

DO - 10.1016/j.jim.2011.01.011

M3 - Article

C2 - 21277306

AN - SCOPUS:79952316511

VL - 366

SP - 69

EP - 78

JO - Journal of Immunological Methods

JF - Journal of Immunological Methods

SN - 0022-1759

IS - 1-2

ER -