Journal: Molecular Vision
Article Title: Temporal ChIP-on-Chip of RNA-Polymerase-II to detect novel gene activation events during photoreceptor maturation
Figure Lengend Snippet: Expression changes (mRNA) of evaluation genes. A-C : Relative mRNA concentrations in the mouse neural retina were measured by qPCR (real time) for the developmental ages P2 and P25. Concentrations were normalized to the beta-Actin mRNA concentration. Bars indicate standard deviation for triplicate assays. Taqman chemistry was used for target specificity with hydrolysis probes that span exon junctions. Rho , Rcvn , Pde6b, and Sag1 are key markers of photoreceptor-specific gene expression. Genes are grouped to account for different scales of relative expression. Most genes had Pol-II peak signal ratios > 1.8, as determined from temporal Pol-II ChIP-on-Chip analysis, except for: Hdac9 (ratio 1.6), Hdac10 (ratio 1.7), and Grik2 (ratio 0.9, Table 1 ). Genes: Rhodopsin (Rho), Recoverin (Rcvrn), Retinoschisis 1 (Rs1), Phosphodiesterase 6b (Pde6b), S-antigen (Sag), Elongation of very long chain fatty acids-like 4 (Elovl4), D4, zinc and double PHD fingers, family 3 (Dpf3), Spectrin repeat containing, nuclear envelope 1 (Syne1), Solute carrier family 38, Na/H -coupled glutamine transporter, member 3 (Slc38a3), Family with sequence similarity 53, member B (A930008G19Rik, Fam53b), Nuclear receptor subfamily 1, group D, member 1 (Nr1d1), Jumonji domain containing 2C (Jmjd2c), Histone deacetylase 9 (Hdac9), Bardet-Biedl syndrome 9 (E130103I17Rik, Bbs9), Histone deacetylase 10 (Hdac10), Glutamate receptor, ionotropic, kainate 2 (beta 2) (Grik2), Solute carrier family 24, Na/K/Ca exchanger, member 1 (Slc24a1).
Article Snippet: Gene expression assays—real-time PCR Specific genes from the ChIP-on-chip data representing a full range of Pol-II peak signal ratios (P25/P2) were analyzed by real-time PCR, using Taqman probe chemistry following the manufacturer’s standard protocol (Applied Biosystems, Foster City, CA).
Techniques: Expressing, Real-time Polymerase Chain Reaction, Concentration Assay, Standard Deviation, Chromatin Immunoprecipitation, Sequencing, Histone Deacetylase Assay