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Comparative analysis of Drd1+ Medium Spiny Neurons, Drd2+ Medium Spiny Neurons, cocaine treatment

ABSTRACT: 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 Comparison

ORGANISM(S): Mus musculus

PROVIDER: GSE13386 | GEO | 2008/11/14

SECONDARY ACCESSION(S): PRJNA113955

REPOSITORIES: GEO

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Comparative analysis of Drd1+ Medium Spiny Neurons and Drd2+ Medium Spiny Neurons

2008-11-14 | GSE13384 | GEO

Comparative analysis of Drd1+ Medium Spiny Neurons and Drd2+ Medium Spiny Neurons

Project 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 Comparison For each cell population, D1 and D2, three independent TRAP replicates were collected, and total RNA from the immunoprecipitates were amplified and hybridized. Data were normalized with the GC-RMA algorithm, and expression values on each chip were normalized to that chip’s 50th percentile. 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.

2008-11-14 | E-GEOD-13384 | biostudies-arrayexpress

Comparative analysis of Drd1+ Medium Spiny Neurons, Drd2+ Medium Spiny Neurons, Motor Neurons, and Purkinje Neurons

2008-11-14 | GSE13387 | GEO

Comparative analysis of Drd1+ Medium Spiny Neurons, Drd2+ Medium Spiny Neurons and whole brain

2008-11-14 | GSE13385 | GEO

Comparative analysis of Drd1+ Medium Spiny Neurons, Drd2+ Medium Spiny Neurons, cocaine treatment

Project 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 Comparison For each cell type and treatment (cell = D1 or D2, treatment = acute or chronic, saline or cocaine) three independent TRAP replicates were collected, and total RNA from the immunoprecipitates were amplified and hybridized. Data were normalized with the GC-RMA algorithm, and expression values on each chip were normalized to that chip’s 50th percentile. 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.

2008-11-14 | E-GEOD-13386 | biostudies-arrayexpress

Comparative analysis of Drd1+ Medium Spiny Neurons, Drd2+ Medium Spiny Neurons, Motor Neurons, and Purkinje Neurons

Project 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 Comparison For each cell population, three independent TRAP replicates were collected, and total RNA from both the immunoprecipitate and unbound fractions were seperately amplified and hybridized. For each tissue, several representative unnbound fractions are provided to serve as controls. Biological replicates are GCRMA normalized within groups. Following averaging of replicates, we recommend further global normalization between groups, using affymetrix biotinylated controls, to correct for any broad biases in scanning and hybridization. Finally for many analyses, we also recommend filtering to remove those probesets with low IP/UB fold change values from each cell type. Researchers can contact us for spreadsheets where these additional steps have been completed.

2008-11-14 | E-GEOD-13387 | biostudies-arrayexpress

Translation profiling time series of mouse Drd1+ medium spiny neurons, Drd2+ medium spiny neurons and whole brain

Project 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. Experiment Overall 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. Experiment Overall Design: Data were normalized withinin two groups (IP and WB) with the GC-RMA algorithm, and expression values on each chip were normalized to that chipâs 50th percentile. Experiment Overall Design: Data were further normalized to the expression values of several positive control genes and to a constant value of 0.01. Experiment Overall Design: Data were then converted to log2 scale. Experiment Overall Design: 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.

2008-11-22 | E-GEOD-13385 | biostudies-arrayexpress

A translational profiling approach for the molecular characterization of CNS cell types

2008-11-14 | GSE13394 | GEO

Transcriptional profiling of medium spiny neurons in the striatum of Drd1-TRAP (CP73) mice administered either saline or cocaine

Project description:TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain. Using this technique we obtained RNA-Seq data from actively translating transcripts present in medium spiny neurons in the whole striatum of adult Drd1-EGFP/Rpl10a (CP73) mice that were administered either saline or cocaine.

2019-12-16 | GSE141424 | GEO

Long-access cocaine intravenous self-administration; transcriptional profiling of medium spiny neurons in the accumbens nucleus of Drd1-TRAP (CP73) mice

Project description:TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain. Using this technique we obtained RNA-Seq data from actively translating transcripts present in medium spiny neurons in the accumbens nucleus of adult Drd1-EGFP/Rpl10a (CP73) mice that were administered either saline or cocaine under long-access conditions

2019-12-16 | GSE141667 | GEO

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