Comment[ArrayExpressAccession] E-GEOD-39697 MAGE-TAB Version 1.1 Public Release Date 2013-12-04 Investigation Title Molecular Signatures of Neurogenesis in the Hippocampal Subgranular Zone of Rodents Comment[Submitted Name] Molecular Signatures of Neurogenesis in the Hippocampal Subgranular Zone of Rodents Experiment Description We sought to find molecular signatures of the SGZ cell types, and to characterize the molecular pathways and transcription factor cascades that define the neurogenic niche. We used laser capture microdissection and DNA microarrays to profile gene expression in the inner (SGZ) and outer portions of the dentate gyrus (DG). Since the vast majority of the cells in the DG are mature granule cells, we compared the expression of the inner and outer portions to reveal molecular markers for the less numerous populations of the SGZ. This data set is part of a larger study assessing conserved molecular signatures of neurogenesis in the hippocampal subgranular zone of rodents and primates. Using a combination of selective SGZ transcriptional profiling with laser microdissection and DNA microarrays as well as in situ hybridization (ISH), we developed an extensive molecular characterization of the mouse SGZ, identifying 367 genes enriched in the SGZ compared to mature granule neurons. These genes displayed a wide range of cellular expression patterns reflecting the cellular milieu of the SGZ, including progenitor and dividing cells, immature granule cells, astrocytes, oligodendrocytes, and GABAergic interneurons. We next used a comparable microarray data set in rhesus monkey that profiled the SGZ across postnatal development to identify genes related to developmentally regulated granule cell neurogenesis. The rhesus monkey SGZ showed highly significant similarity to mouse, whereas network analysis of these data identified SGZ-enriched gene sets with different temporal profiles reflecting differential time-courses for maturation of glia and granule neurons. One neurogenesis-related gene network showed a steady decrease in expression across postnatal rhesus development from birth to adulthood. This temporal pattern is highly correlated with the number of proliferating cells in the dentate gyrus, and the neurogenic transcription factors Sox4 and Sox11 are central hub genes for this gene network. A number of the genes in this network showed a similar postnatal downregulation in mouse, suggesting a general conservation of molecular mechanisms underlying developmental and adult neurogenesis in rodents and primates. Primate data available at: http://www.blueprintnhpatlas.org/ Brains from 10- to 11-week-old C57BL/6 male mice housed in three conditions (no running, 4 days of running, 30 days of running) were sectioned and the dentate gyrus was isolated. For each brain, the inner granule cell layer (containing the subgranular zone) and outer GCL were separated using laser capture microdissection, and RNA from each region was collected and processed as described in the protocols. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Miller Nathanson Miller Lein Gage Person First Name Jeremy Jason Jeremy Ed Fred Person Mid Initials A S H Person Email jeremyinla@gmail.com Person Affiliation Allen Institute for Brain Science Person Address Allen Institute for Brain Science, 11501 N Park Ave N, Seattle, WA, USA Person Roles submitter Protocol Name P-GSE39697-1 P-GSE39697-4 P-GSE39697-5 P-GSE39697-2 P-GSE39697-3 P-GSE39697-6 Protocol Description Initial data analysis and normalization were done using the Affymetrix Expression Console using two algorithms: Robust Multichip Analysis (RMA) and Probe Logarithmic Intensity Error Estimation (PLIER) using the minus mismatch option (-MM). Note that an additional filtering step to remove the effect of running was performed in the larger cross-species study, using ComBat (www.bu.edu/jlab/wp-assets/ComBat). ID_REF = VALUE = RMA normalized signal intensity 5ng total RNA starting material was amplified using the MessageAmp aRNA Kit (Ambion Inc, Austin, TX). This method utilizes reverse transcription with T7 RNA Polymerase. The first and second rounds of the kit were performed per the manual, with an additional third round identical to the second round except that the in vitro transcription step utilized the Enzo BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA). 15μg of biotinylated aRNA was fragmented and hybridized to Affymetrix MG-U74Av2 arrays. Brains were quickly removed, flash-frozen in OCT mounting medium in a dry ice-isopentantane slurry, and stored at -80C until use. 12μm thin cryostat sections were stained with cresyl violet, rapidly dehydrated through xylenes, and stored until use a vacuum dessicator. An Arcturus PixCell II machine (Arcturus, Mountain View, CA) was used to isolate 2-3 cell thick bands from both the inner and outer portions of the dentate granule cell layer. Total RNA was purified from the laser captured tissue using the Absolutely RNA Nanoprep Kit (Stratagene, La Jolla, CA), and RNA yield was assessed using the RiboGreen RNA Quantitation Reagent (Molecular Probes Inc, Eugene, OR). RNA from three groups of animals (no running, 4 days of running, 30 days of running), consisting of 3 animals each, was isolated independently and amplified separately. Gene chips were scanned following the manufactures protocol. Protocol Type normalization data transformation protocol labelling protocol hybridization protocol sample treatment protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name REGION DAYS_RUNNING ANIMAL Experimental Factor Type region days_running animal Publication Title Conserved molecular signatures of neurogenesis in the hippocampal subgranular zone of rodents and primates. Publication Author List Miller JA, Nathanson J, Franjic D, Shim S, Dalley RA, Shapouri S, Smith KA, Sunkin SM, Bernard A, Bennett JL, Lee CK, Hawrylycz MJ, Jones AR, Amaral DG, Sestan N, Gage FH, Lein ES PubMed ID 24154525 Publication DOI 10.1242/dev.097212 Comment[SecondaryAccession] GSE39697 Comment[GEOReleaseDate] 2013-12-04 Comment[ArrayExpressSubmissionDate] 2012-07-27 Comment[GEOLastUpdateDate] 2013-12-04 Comment[AEExperimentType] transcription profiling by array SDRF File E-GEOD-39697.sdrf.txt