면역학적 문제들, 예를 들면 T cell activation과정, Immunologic Memory, Tolerance등에 관한 Genomics적 접근들을 검토해본다.

Exercise in cDNA microarray data analysis using an interesting public dataset

Dataset published in PNAS 99; 11796-11801 by Diehn, M et al.(2002)

1. Study Object

To characterize the genomic expression program in human peripheral T cells responding to stimulation of both the antigen-specific T cell receptor and a second coreceptor such as CD28.

Detailed informations can be found in the author's web site: http://genome-www.stanford.edu/costimulation

2. Experimental Design

Reference sample: Pooled from human primary T cells and the human Jurkat leukemia cell stimulated for varying times with ionomycin and PMA

Treatment sample: Peripheral blood T cells were subjected to six distinct treatments in parallel time series and harvested at seven time intervals (0,1,2,6,12,24, and 48hr)

Six distinct treatments: 1) no stimulus; 2) stimulation with αCD3; 3) stimulation with αCD28; 4) stimulation with αCD3       and αCD28; 5) treatment with 5 μg/ml of phytohemagglutinin(PHA); 6) treatment with ionomycin[1μM]/PMA[25ng/ml]

3. Preprocessing (for between chip comparisons)

- spots with non-zero flags are removed from the analysis

- background pixel median is subtracted from foreground pixel median intensity

- variance stabilization transformation is performed and within pin group lowess normalization is done to achieve location normalization

- scale normalization is done

file after preprocessing

4. Further analyses