90K Combimatrix microarray were synthesized using the Combimatrix synthesizer (Combimatrix) that allows in-situ synthesis of oligonucleotide probes through the phosphoramidites chemistry.
Description
Concerning mRNAs Ensembl transcripts (Ver. 56) and UniGene (Ver. 38) sequences were used to produce a pig 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. We obtained probes with different specificity and different distances from the mRNA 3 -end. The two best probes for every sequence, basing on the reliability of the prediction algorithm and their vicinity to the 3 -end were experimentally tested for their specificity and performance (GEO: ..). For any transcript with a replicated probe, we selected the probe that was the most responsive and specific in a hybridization trial performed with a pool of mRNAs from 20tissues. The specificity was based on the intensity fluorescence, as suggested by Kronick (Kronick 2004). Replicated probes with higher intensity fluorescence were considered the most responsive for the specific gene. The resulting whole genome microarray, here used for the gene expression analysis, was composed by 17,048 replicated probes and 963 not replicated specific for the Ensembl transcripts, 11,363 replicated probes specific for the UniGene clusters of length comprised between 778 nt and 1,348 nt (Figure SM1), and 28,790 single probes specific for the remaining UniGene clusters. All probes mapped proximally to the 3 end of the target sequences (Figure SM2 A and SM2 B): 98.2% of the probes for the Ensembl transcripts mapped within 2,000 nt from their 3 end while the percentage for UniGene clusters reached 99.9%. 114 UniGene clusters and 1,592 Ensembl transcripts were not identified by specific probes.
Discovering, evolution, biogenesis, expression and target prediction of porcine micro-RNAs: new regulatory gene expression network in different tissues.
Data table header descriptions
ID
Array #
Number of the array
Feature #
Number of the spot
Column
Number of the array column
Row
Number of the array row
Probe #
Number of the probe
Name
Probe name
sequence id
Ensembl transcript ID or ID of the used sequence to identify the probe and representing the corresponding UniGene cluster. If the probe identify two Ids these are separated by |
Ensembl id
Ensembl transcript ID
UniGene id
UniGene ID
Ensembl Gene
Ensembl gene ID
entrez
Entrez gene ID
symbol
Gene symbols
Alias
Gene aliases
RefSeq mRNA
mRNA RefSeq ID
refSeq peptide
RefSeq peptide ID
Description
Gene description
Alternative descriptions
Gene description derived from aliases or UniGene database
