Transcription profiling of mouse ATCC CRL1606 hybridoma cells to evaluate microarray gene identification methods using spike-in experiments

ABSTRACT: Due to the lack of controlled microarray experimental data, evaluation of gene identification methods has been performed using simulated/manipulated data. As the ability of these approaches to mimic actual experimental data is questionable, conclusions drawn can be misleading. We applied spike-in approaches to develop experimental benchmark data and used it to evaluate various gene identification methods.

mRNA was obtained from mouse ATCC CRL1606 hybridoma cells. From self hybridization results 200 genes that consistently exhibited a log ratio value close to 0 were randomly selected across a range of intensity. In-vitro transcripts of these 200 genes were obtained from their respective clones. From RNA gel electrophoresis and test array results, 169 of the 200 transcripts were deemed successful. Experiments were then conducted by spiking these 169 transcripts to the common pool of mRNA extracted from the hybridoma cells. With exception of the spiked in genes, the experimental set-up is identical to a self hybridization. This experiment is thus different from other microarray experiments as the set of differentially expressed genes is known as they have been artificially created.

ORGANISM(S): Mus musculus

SUBMITTER: Althea Chua 

PROVIDER: E-MEXP-280 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress