Identification of responsive probes for mRNA transcripts of the pig (S. scrofa) genome

ABSTRACT: Pig mRNAs Ensembl transcripts (Ver. 56) and UniGene (Ver. 38) sequences were used to produce a dedicated microarray platform to analyze mRNAs gene expression. Based on sequence similarity we rejected UniGene features that overlapped more than 40% with an Ensembl transcript. After this filter we obtained 40,267 UniGene clusters and 19,603 Ensembl transcripts (protein coding + pseudogenes + retrotransposed elements). Starting from these sequences, the microarray probes were computed using 6 different algorithms (YODA, Picky, ArrayOligoSelector, OligoPicker, OligoFaktory, CommOligo). Two probes in the most 3M-bM-^@M-^Y end was tested for their specificity and performance. For any transcript with a replicated tested probe, we used the most responsive and specific in an hybridization trial with

ORGANISM(S): Sus scrofa

SUBMITTER: Gerolamo Lanfranchi 

PROVIDER: E-GEOD-28636 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress