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E-GEOD-33085 - Transcriptome analysis of adult retina cell types

Status
Released on 30 November 2011, last updated on 2 March 2012
Organism
Mus musculus
Samples (78)
Array (1)
Protocols (7)
Description
Brain circuits are assembled from a large variety of morphologically and functionally diverse cell types. It is not known how the intermingled cell types of individual brain regions differ in their expressed genomes. Here we describe an atlas of cell type transcriptomes of the adult retina. We found that each adult cell type expresses a specific set of genes, including a unique set of transcription factors, forming a “barcode” for cell identity. Cell type transcriptomes carry enough information to categorize cells into corresponding morphological classes and types. Surprisingly, several barcode genes are eye disease-associated genes that we demonstrate to be specifically expressed not only in photoreceptors but also in particular retinal circuit elements such as inhibitory neurons as well as in retinal microglia. Our data suggest that distinct cell types of individual brain regions are characterized by marked differences in their expressed genomes. We assembled a library of 22 transgenic mouse lines in which each line had a group of retinal cells marked with fluorescent proteins. We built up the library with the purpose of having some mouse lines in which single retinal cell types and others in which combinations of types from a single class are labeled. The library had mouse lines with labeled cells representing each of the six retinal cell classes. Retinal cells were characterized by physiological recording and immunohistochemical staining. We isolated 200 fluorescent protein-labeled retinal cells (“cell groups”) from at least three different mice of each mouse line by fluorescence-activated cell sorting. The transcripts of each cell group of these biological triplicates were independently amplified in batches. Each batch contained an internal control cell group from the Arc-line. We performed gene expression analysis of 22 transgenic mouse lines. All experiments were performed in biological triplicates. Gene expression analysis was performed in 3 batches. Arc is the batch control (1st, 2nd, 3rd). B2 was repeated 3 times.
Experiment type
transcription profiling by array 
Contacts
Sandra Siegert <ssiegert@mit.edu>, Botond Roska, Erik Cabuy
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-33085.idf.txt
Sample and data relationshipE-GEOD-33085.sdrf.txt
Raw data (2)E-GEOD-33085.raw.1.zip, E-GEOD-33085.raw.2.zip
Processed data (1)E-GEOD-33085.processed.1.zip
Array designA-AFFY-130.adf.txt
Links