title: Mouse strain specific gene expression differences for illumina microarray expression profiling in embryos.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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 the sensitivity of the array towards the genetic background. Consistent strain sensitivity of some probes was attributed to genetic polymorphisms or probe design related artifacts.
  
  
  CONCLUSIONS
  Our study provides an extensive reference list of gene expression profiling background noise of value to anyone in the field of developmental biology and transgenic research performing microarray expression profiling with the widely used Illumina microarray platform. Probes identified as strain specific background noise further allow for microarray expression profiling on its own to be a valuable tool for establishing genealogies of mouse inbred strains.
authors.affiliation: Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore 138672, Singapore.
authors.forename: Petra
authors.initials: P
authors.lastname: Kraus
authors.forename: Xing
authors.initials: X
authors.lastname: Xing
authors.forename: Siew Lan
authors.initials: SL
authors.lastname: Lim
authors.forename: Max E
authors.initials: ME
authors.lastname: Fun
authors.forename: V
authors.initials: V
authors.lastname: Sivakamasundari
authors.forename: Sook Peng
authors.initials: SP
authors.lastname: Yap
authors.forename: Haixia
authors.initials: H
authors.lastname: Lee
authors.forename: R Krishna Murthy
authors.initials: RK
authors.lastname: Karuturi
authors.forename: Thomas
authors.initials: T
authors.lastname: Lufkin
mesh_terms: D000818:Animals; D001483:Base Sequence; D004622:Embryo, Mammalian / Q000378:metabolism*; D020869:Gene Expression Profiling; D051379:Mice; D008822:Mice, Transgenic; D020411:Oligonucleotide Array Sequence Analysis; D013045:Species Specificity