Transcription profiling of two rat cell lines using different blocking reagents and doses to optimize cDNA microarray procedures without using an external standard

ABSTRACT: We performed a dye-swap microarray experiment using a total of 24 Rat 15k cDNA duplicates microarrays. The study included RNA from samples with high expected differential gene expression termed ‘high contrasts’ compared to self-self hybridization (rat cell lines AR42J and NRK52E). We than optimized a pipeline to maximize the number of genes found differentially expressed between the two different RNA samples while at the same time making sure that the methodology finds no differentially expressed genes in self–self experiments with the same cell lines. In this high-contrast vs. self-self method (HCSSM) significantly expressed genes is determined by estimating the false discovery rate (FDR) using a null distribution obtained from self-self experiment. The optimization criterion requires onl

ORGANISM(S): Rattus norvegicus

SUBMITTER: Hallgeir Bergum 

PROVIDER: E-TABM-202 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress