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GSE23796
Mus musculus
4 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
We used wild-type neurons, and directly compared neurons that had been infected with lentiviruses expressing the CaM shRNAs either without or with a wild-type CaM rescue protein. We then analyzed the gene expression patterns in these neurons with the Affymetrix mouse gene ST_1.0 chip. We identified in two independent array studies ~250 genes whose expression was consistently up- or down-regulated by the CaM KD, as compared to the CaM KD/rescue control. As expected, multiple classes of genes were regulated by CaM. Consistent with previous studies, we found that activity-dependent genes, such as Homers, Npas2, Arc and Egr3, were down-regulated by the CaM KD. Interestingly, we observed that several synaptic trafficking proteins were either up- or downregulated by the CaM KD. Among these was a large increase in the expression of Syt2, which can serve as a Ca2+-sensor for synaptic exocytosis; thus, this upregulation of Syt2 by the CaM KD likely accounts for the rescue of the Syt1 KO phenotype. In addition, expression of Syb1 was massively increased, whereas expression of Syt4, Syt9, and syntaxin-1A was decreased. Another intriguing class of proteins whose expression was strongly regulated by CaM were cell-adhesion molecules, such as the synaptic cell-adhesion molecules Lrrtm1, Lrrtm3, and contactin-2. Moreover, we observed up-regulation of sodium channels, and a down-regulation of potassium channels, suggesting that CaM might control the activity-dependent regulation of neuronal excitability. Finally, we detected changes in multiple genes encoding transcription factors, intracellular signal transduction proteins, elements of the cytoskeleton, or metabolic enzymes. It should be noted, however, that despite these multifarious changes, more than 95% of genes showed no CaM KD-induced change, suggesting that the observed CaM KD-dependent expression changes are specific.
Publication Title
Calmodulin suppresses synaptotagmin-2 transcription in cortical neurons.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 103 Downloadable Samples
NextSeq 500
Description
Recent advances in single-cell RNAseq technologies are enabling new cell type classifications. For neurons, electrophysiological properties traditionally guide cell type classification but correlating RNAseq data with electrophysiological parameters has been difficult. Here we demonstrate RNAseq of electrophysiologically and synaptically characterized individual, patched neurons in the hippocampal CA1-region and subiculum, and relate the resulting transcriptome data to their electrical and synaptic properties. In this analysis, we explored the hypothesis that precise combinatorial interactions between matching cell-adhesion and signaling molecules shape synapse specificity. In analyzing interneurons and pyramidal neurons that are synaptically connected, we identified two independent, developmentally regulated networks of interacting genes encoding cell-adhesion, exocytosis and signal-transduction molecules. In this manner, our data allow postulating a presumed cell-adhesion and signaling code, which may explain neuronal connectivity at the molecular level. Our approach enables correlating electrophysiological with molecular properties of neurons, and suggests new avenues towards understanding synaptic specificity. Overall design: These data include 15 tissue samples (including 3 independent replicas in 5 developmental stages) as well as 93 single-cell samples (including CA1 cholecystokinin, parvalbumin, and pyramidal neurons as well as subiculum burst and regular firing pyramidal neurons).
Publication Title
Single-cell RNAseq reveals cell adhesion molecule profiles in electrophysiologically defined neurons.
Sample Metadata Fields
Specimen part, Disease, Subject
View Samples- Mus musculus
- 16 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Gene expression analysis of 2-month-old APP/APLP2 double-conditional Knockout (N-dCKO) mice and littermate APLP2 knockout controls, APP knockout and wildtype controls.
Publication Title
Soluble amyloid precursor protein (APP) regulates transthyretin and Klotho gene expression without rescuing the essential function of APP.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- NextSeq 500
Description
Examining the transcriptomic changes during transdifferentiation of peripheral blood mononuclear cells to induced neuronal cells. Overall design: There are three different populations: PBMC (2 biological replicates, starting population), PSA-NCAM+GFP+ (2 biological replicates, induced neuronal cells) and PSA-NCAM+GFP- (2 biological replicates, induced neuronal cells).
Publication Title
Transdifferentiation of human adult peripheral blood T cells into neurons.
Sample Metadata Fields
Specimen part, Subject
View Samples