Microarray Gene expression arrays Mouse liver tissue

Get tips on using GeneChip™ Rat Genome 230 2.0 Array to perform Microarray Gene expression arrays - Rat mesothelium Satin cocktail

DNA-protein interactions are studied by using ChIP. The basic steps in this technique are crosslinking, sonication, immunoprecipitation, and analysis of the immunoprecipitated DNA. During ChIP, if chromatin is under-fragmented or fragments are too large which can lead to the increased background and lower resolution. Shorter cross-linking times (5-10 min) and/or lower formaldehyde concentrations (<1%) may improve shearing efficiency. If Chromatin is over-fragmented, then optimize shearing conditions for each cell type to improve ChIP efficiency. Over-sonication of chromatin may disrupt chromatin integrity and denature antibody epitopes. If you do not see any product or very little product in the input PCR reactions, add 5–10 μg chromatin per IP.

Get tips on using SurePrint G3 Mouse Exon 4x180K Microarray Kit (165,984 Exon probes) to perform Microarray Mice - Cochlea Expression array (labelled)

Get tips on using GeneChip™ Hybridization, Wash, and Stain Kit to perform Microarray Gene expression arrays - Rat mesothelium Satin cocktail

Get tips on using GeneChip® Human Genome U133 Plus 2.0 Array to perform Microarray Gene expression arrays - Human endometrial stromal cells Biotin

Get tips on using SurePrint G3 Mouse GE 8x60K Microarray Kit to perform Microarray Comperative genomic hybridization - Mouse iPSC

Microarrays enable researchers to monitor the expression of thousands of genes simultaneously. However, the sensitivity, accuracy, specificity, and reproducibility are major challenges for this technology. Cross-hybridization, combination with splice variants, is a prime source for the discrepancies in differential gene expression calls among various microarray platforms. Removing (either from production or downstream bioinformatic analysis) and/or redesigning the microarray probes prone to cross-hybridization is a reasonable strategy to increase the hybridization specificity and hence, the accuracy of the microarray measurements.

The estimation of DNA methylation level heavily depends on the complete conversion of non-methylated DNA cytosines. It is crucial to ensure complete conversion of non-methylated cytosines in DNA. Therefore, it is important to incorporate controls for bisulfite reactions, as well as to pay attention to the appearance of cytosines in non-CpG sites after sequencing, which is an indicator of incomplete conversion.