Journal: BMC Genomics

Article Title: Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton

doi: 10.1186/1471-2164-8-294

Figure Lengend Snippet: Microarray platform features

Article Snippet: We used 25-mer oligonucleotide commercial chips (Affymetrix, human genome U133A 2.0) and academic arrays prepared with a 70-mer oligonucleotide set (Operon, human whole genome version 2.0).

Techniques: Microarray, Sequencing

Journal: BMC Genomics

Article Title: Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton

doi: 10.1186/1471-2164-8-294

Figure Lengend Snippet: Microarray platform comparison . Series of expression profiling assays were performed using the HG-U133A 2.0 Affymetrix GeneChip (3 replicates per RNA sample), the human oligonucleotide Operon set (4 replicates) and the Actichip arrays (10 replicates). Experiments were carried out using the same lots of RNAs extracted from human carcinoma MCF-7 cell line and from human skeletal muscle. Data were analysed as stated in the "Methods" section resulting in two groups of genes : "detected" and "not detected". The genes found similarly expressed or not expressed in less than 2/3 of the replicated assays were deemed "non reproducible". The histograms show the distribution of the three groups of genes for each platform relative to the samples. Results are expressed as percentages relative to the total number of genes simultaneously represented on each array platform.

Article Snippet: We used 25-mer oligonucleotide commercial chips (Affymetrix, human genome U133A 2.0) and academic arrays prepared with a 70-mer oligonucleotide set (Operon, human whole genome version 2.0).

Techniques: Microarray, Expressing

Journal: BMC Genomics

Article Title: Identification of SNPs and INDELS in swine transcribed sequences using short oligonucleotide microarrays

doi: 10.1186/1471-2164-9-252

Figure Lengend Snippet: a, b: Theoretical outcomes of probe hybridization . A) Affymetrix short oligonucleotide arrays are fabricated with sets of eleven 25-mer probes to interrogate the expression level of a particular mRNA. Because of the short probe length, a SNP falling in the middle of the probe sequence will result in that probe's failure to hybridize. B) Three potential hybridization scenarios within a single probe set are depicted: 1) mRNA to target probes is not expressed in either breed, 2) mRNA to target probes is equivalent in both breeds or, 3) intensity of probes is expressed in one breed and negligible in the other breed. In this latter case, a probe-by-breed effect is seen with Meishan RNA hybridized to probe 2 of the probe set. The green hash represents the SFP located within a central nucleotide position within the probe.

Article Snippet: Recently, chip-based methods [ - ] (and references [ - ]) such as Affymetrix gene expression arrays have been used for SNP discovery Affymetrix short oligonucleotide arrays are fabricated with sets of eleven 25-mer probes to interrogate the expression level of a particular mRNA.

Techniques: Hybridization, Expressing, Sequencing