Journal: PLoS ONE

Article Title: Down Regulation of Genes Involved in T Cell Polarity and Motility during the Induction of Heart Allograft Tolerance by Allochimeric MHC I

doi: 10.1371/journal.pone.0008020

Figure Lengend Snippet: The allograft T Cell microarray data were analyzed by PCA using Partek Genomics Suite. 50% of the variation in samples was revealed in the first two principal components. The first principal component is represented by the X axis and the second principal component by the Y axis. Treatment type appeared to be major source of variation and is indicated by different colored ellipsoids. Green, untreated; Red, CsA only; and Blue, CsA plus peptide. The numbers next to each ellipsoid indicate the number of days post transplantation regardless of treatment type. The type of treatment appeared to be the most significant effect and the treatment time was another significant variable. Each treatment could be seen as distinct groups. Both the untreated (Green) and the cyclosporine treated (Red) samples seemed to form similar cluster shapes. Cyclosporine plus peptide (Blue) sample, on the other hand, was much more spread out. This could be due to another variable such as time after transplantation. Indeed, treatment time did appear to have some effect on the PCA since the ovoids representing 7 day-treatment samples were always to the left of the 1 or 3 days treatments.

Article Snippet: The microarray hybridization and analysis were performed by Cogenics (Morrisville, NC) according to the manufacturer's protocol (Affymetrix, Santa Clara, CA).

Techniques: Microarray, Transplantation Assay

Journal: BMC Genomics

Article Title: ChIP on Chip: surprising results are often artifacts

doi: 10.1186/1471-2164-11-414

Figure Lengend Snippet: Detection of critical steps in the ChIP-Chip protocol . A Ratios of ChIP DNA purified with spin column versus column free purified DNA detected by qPCR for the indicated gene regions. B qPCR ratios of crosslinked-reversed versus non crosslinked DNA for indicated gene regions. C Crosslinked-reversed versus non crosslinked DNA as shown in B was differentially labeled and hybridized to a microarray. Log 2 ratios are shown in blue (only values below -0.5) in comparison to the SeqA ChIP signal (from Fig. 2).

Article Snippet: We thank Franz Narberhaus (Bochum) for the σ 32 antiserum and Douglas Hurd (Oxford Gene Technology) for instruction in DNA labeling and microarray hybridization.

Techniques: ChIP-chip, Purification, Labeling, Microarray, Comparison