Mouse strain specific gene expression differences for illumina microarray expression profiling in embryos.

BMC Research Notes
P KrausThomas Lufkin

Abstract

In the field of mouse genetics the advent of technologies like microarray based expression profiling dramatically increased data availability and sensitivity, yet these advanced methods are often vulnerable to the unavoidable heterogeneity of in vivo material and might therefore reflect differentially expressed genes between mouse strains of no relevance to a targeted experiment. The aim of this study was not to elaborate on the usefulness of microarray analysis in general, but to expand our knowledge regarding this potential "background noise" for the widely used Illumina microarray platform surpassing existing data which focused primarily on the adult sensory and nervous system, by analyzing patterns of gene expression at different embryonic stages using wild type strains and modern transgenic models of often non-isogenic backgrounds. Wild type embryos of 11 mouse strains commonly used in transgenic and molecular genetic studies at three developmental time points were subjected to Illumina microarray expression profiling in a strain-by-strain comparison. Our data robustly reflects known gene expression patterns during mid-gestation development. Decreasing diversity of the input tissue and/or increasing strain diversity raised...Continue Reading

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Citations

Aug 12, 2014·PloS One·Petra KrausLawrence W Stanton
Feb 19, 2013·Developmental Biology·Petra KrausThomas Lufkin
Apr 4, 2015·Mediators of Inflammation·Agata SzadeAlicja Józkowicz
Apr 29, 2016·Genesis : the Journal of Genetics and Development·Al-Sayed Al-SoudyFumihiro Sugiyama
Feb 13, 2014·Molecular and Cellular Biochemistry·Jarinthorn TeerapornpuntakitNarattaphol Charoenphandhu
Nov 6, 2018·Toxicology and Applied Pharmacology·Lana ShayaJoanna Y Wilson
May 15, 2021·Journal of Mammary Gland Biology and Neoplasia·Samantha HenryCamila O Dos Santos
May 19, 2021·Translational Vision Science & Technology·Mingxue ZhouChao Ma

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Methods Mentioned

BETA
transgenic
dissection
PCR
chip
nucleotide exchange
RNA-seq
electrophoresis
reverse transcription PCR

Software Mentioned

Bioanalyzer
Vector NTI Advance 10
mapview
Affymetrix
GenomeStudio
Cluster
TreeView
Limma
BLAST
- Like Alignment Tool ( BLAT )

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