Project description:Differential gene expression between naive and activated CD8+ T cells was assessed using microarray analysis to determine target genes for new positron emission tomography (PET) probe screening, in particular for molecular imaging of lymphoid organs and immune activation. Experiment Overall Design: Total RNA was purified from tissues using the Qiagen RNeasy Mini kit. Total RNA was extracted from purified naïve and proliferating (72 hrs post activation) CD8+ T cells from the pmel-1 TCR transgenic mice. Pooled RNA from 4 independent experiments was hybridized to Affymetrix Mouse Genome 430 2.0 arrays. Absolute calls describing whether a probe set is present (P), marginally present (M), or absent (A) were generated using the Affymetrix GeneChip Operating Software v1.3 (GCOS) and expression values were calculated using the PM/MM difference model of DNA-Chip (dChip). Expression values across samples were normalized using dChipâ??s invariant set method. A gene was considered differentially expressed if the corresponding probe set fit the following criteria: absolute call was P in at least half of the samples, fold change >1.4 between baseline (naïve CD8+ T cells) and experimental (activated CD8+ T cells) using the lower 90% confidence bound of fold change as defined in dChip, and expression difference between the baseline and experimental samples was >100. Genes involved in the nucleoside de novo biosynthesis and salvage pathways were taken from the KEGG database (pathway IDs 00230 and 00240), and corresponding probe sets were manually extracted from Affymetrixâ??s NetAffx to ensure complete coverage of all nucleoside pathway genes (239 probe sets), plus the SLC28 and SLC29 transporters (10 probe sets).
Project description:Screening for mouse cDNA that was highly expressed in positive-selector H-2b AND-TCR-transgenic thymocytes using Affymetrix Murine Genome arrays. Experiment Overall Design: 2 thymocytes, H-2b AND-TCR-transgenic thymocytes and C57BL/6 thymocytes, were analyzed by duplicate hybridization.
Project description:Screening for mouse cDNA that was highly expressed in positive-selector H-2b AND-TCR-transgenic thymocytes using Affymetrix Murine Genome arrays. Keywords: transgenic mouse
Project description:Transcriptome analysis of M. quadriceps of Mus musculus after HSA (human α-skeletal actin promoter)-driven transgenic overexpression of CRK.
Project description:To identify the molecular bases for divergence in differentiation programs of naïve CD8 T cells, we monitored gene expression profile of CD8+ T cells from BM3.3 transgenic mice during responses to TCR ligands of different avidity (full response with antigen presenting cells from C57BL/6 mice , partial response with antigen presenting cells from C57BL/6.C-H-2bm8 mice).