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E-GEOD-46373 - Change of fate comitment in adult neural progenitor cells subjected to chronic inflammation

Status
Released on 9 September 2014, last updated on 14 September 2014
Organism
Rattus norvegicus
Samples (54)
Array (1)
Protocols (6)
Description
Neural progenitor cells (NPCs) have regenerative capabilities that are activated during inflammation. By measuring the global transcriptome and performing functional studies, we aimed at elucidating if and how NPCs from the non-germinal niche of the spinal cord differ from germinal niche NPCs, here represented by the subventricular zone (SVZ) NPCs. Moreover, we investigated how these cells are affected by chronic inflammation modeled by Experimental Autoimmune Encephalomyelitis (EAE). NPCs were isolated and propagated from the SVZ and cervical, thoracic and caudal regions of the spinal cord from healthy rats and rats subjected to EAE. Using Affymetrix microarray analyses, the global transcriptome was measured in the different NPC populations both in undifferentiated and differentiated cultures. These analyses were paralleled by differentiation studies and quantitative RT-PCR of differentiation-specific genes. In NPCs isolated from healthy rats, transcriptional and functional analyses revealed a higher neurogenic potential in SVZ-derived NPCs compared to spinal cord NPCs. The neurogenicity of spinal cord NPCs was increased by exposure to the inflammatory environment. Concurrently, their gliogenicity was decreased which was supported by a decreased expression of glial differentiation signature genes and related signaling pathways. Differentiation analyses showed that spinal cord NPCs from EAE rats generated fewer oligodendrocytes and astrocytes than NPCs isolated from healthy controls. 54 samples were analysed. The transcriptome of NPCs isolated from healthy rats or rats with EAE was measured. The NPCs were isolated from the SVZ and the cervical, thoracic and caudal parts of the spinal cord. Pair wise student t-test analysis between the 3 EAE replicates and naive controls for each respective tissue type was performed. Genes with a signal value above the cut-off of 50 and with FDR ≤ 5% and a foldchange of ≥1.2 or ≤-1.2 were selected for further analysis.
Experiment type
transcription profiling by array 
Contacts
Ruxandra Covacu <ruxandra.covacu@ki.se>, Cynthia Perez Estrada, Lisa Arvidsson, Lou Brundin, Mikael Svensson
Citation
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-46373.idf.txt
Sample and data relationshipE-GEOD-46373.sdrf.txt
Raw data (2)E-GEOD-46373.raw.1.zip, E-GEOD-46373.raw.2.zip
Processed data (1)E-GEOD-46373.processed.1.zip
Additional data (1)E-GEOD-46373.additional.1.zip
Array designA-GEOD-6247.adf.txt
Links