Project name: Mus musculus

Description: The cellular heterogeneity of the brain confounds efforts to elucidate the biological properties of distinct neuronal populations.Using Bacterial Artificial Chromosome (BAC) transgenic mice which express EGFP-tagged ribosomal protein L10a in defined cell populations, we have developed a methodology to affinity purify polysomal mRNAs from genetically defined cell populations in the brain.The utility of this approach is illustrated by the comparative analysis of four types of neurons, revealing hundreds of genes that distinguish these four cell populations.We find that even two morphologically indistinguishable, intermixed subclasses of medium spiny neuron display vastly different translational profiles and present examples of the physiological significance of such differences.This genetically targeted Translating Ribosome Affinity Purification (TRAP) methodology is a generalizable method useful for the identification of molecular changes in any genetically defined cell type in response to genetic alterations, disease, or pharmacological perturbations.Keywords: Cell Type ComparisonOverall design: For each RNA source (D1, D2, and WB), three independent TRAP or total RNA replicates were collected, and total RNA from the immunoprecipitates or homogenized tissue was amplified and hybridized.Data were normalized withinin two groups (IP and WB) with the GC-RMA algorithm, and expression values on each chip were normalized to that chip’s 50th percentile.Data were further normalized to the expression values of several positive control genes and to a constant value of 0.01.Data were then converted to log2 scale.We recommend that only genes where more than one sample has a normalized intensity larger than 16 (4 in log2 scale) should be kept in the analysis.

Data type: Transcriptome or Gene expression

Sample scope: Multiisolate

Relevance: ModelOrganism

Release date: 2008-11-14

Last updated: 2008-10-28